Here's my idea......firstly, base the faction abilities off of the Planewalker, Dragon Magazine, Planar Handbook, and old Planescape materials, but make each ability something like 1-3 feats in equivalance, if you can. For comparison, I tend to consider the ability to cast a single 3rd-level spell each day to be worth a feat, i.e. being able to Fireball a dozen orcs for 10d6 damage once per day in place of being able to Great Cleave through said orcs all day long. At least as a rough approximation, but it gives you a baseline to think about.
Now then, as for balancing the abilities against the characters.......
I'd suggest having each faction ability impose a certain percentage XP penalty or, if you prefer, a certain hard XP sink, either way based on the level the faction ability is gained at and based on the potency of the faction ability. Now, you may decide to use a single unified set of guidelines for this, or perhaps personalize it to each faction as needed (i.e. if you can't think of/justify so many abilities, or so few but powerful abilities, for a certain faction, then maybe that faction should grant abilities at a different rate and of appropriately different power levels). You might incorporate some drawbacks to a few, or perhaps many, faction abilities as appropriate. Keep in mind though that joining a faction should, overall, provide more advantages than penalties, so any drawbacks or other balancing factors should be slightly weaker than the benefits gained in exchange.
Most of what follows will describe the first idea in more detail, then I'll add a note about the simpler (or at least easier to explain) second idea, and then an example of some sort.
Allow me to explain in more detail what I meant above....... The first idea is to impose a percentage penalty on all Experience Points earned henceforth after gaining each faction ability. For instance, after gaining the 1st ability of a faction, the character henceforth suffers an X% penalty to XP earned, and when they later gain the 2nd faction ability they add Y% to the XP penalty, making it a penalty of X+Y %. I.E. perhaps a 5% XP penalty the first time, then compounded by a further 10% penalty from the 2nd faction ability, then compounded by another 10% XP penalty with the 3rd faction ability, totalling 25% by that point. Just for example, definitely not the simplest route (which would be to instead make it a solid 10, 20, 25, 35, or 50% penalty every time).
Going for the XP penalty would have another bit of balancing to make this work, though: every time the character's total XP penalty from faction abilities reaches, say, 30% (you may need to do some trial and error testing to find a better workable percentage), they immediately reduce their total faction-based XP penalty by 30% (or whatever number you use for the aforementioned point) and acquire in its place a +1 Level Adjustment that does not affect their current level (unlike a normal LA however, it would not affect how many XP they need for their current level, just for further levels; in the case of being level drained or suffering other level loss, consider the faction-based LA to still not affect XP needed for the level at which that particular point of faction LA was acquired).
Thus, if we say for example that PC Bob accumulates a 15% XP penalty from their 1st faction ability, then a further 5% from their next faction ability, then another 15% from the 3rd faction ability, they immediately reduce their XP penalty by 30% for a new penalty of just 5% but also a new +1 Level Adjustment.....then when PC Bob later gains a 10% XP penalty from their 4th faction ability, another 10% penalty from his 5th faction ability, and a 20% XP penalty from his 6th faction ability, he reduces that by 30% and has a new total faction XP penalty of 15%, but also now has a total faction-based +2 Level Adjustment.
You'll have to try some calculations, or some trial sessions, with these mechanics to determine the best amount of XP penalty to impose for faction abilities, and the best amount of such penalty at which to swap out a like amount for a Level Adjustment. For a point of reference, I've calculated previously that a 10% XP Penalty, imposed right from the start, is practically the same as a +1 Level Adjustment in the total XP required to reach 20th-level. That is, a character who needs to earn 10% more XP to level each time will eventually, by 20th-level, have acquired approximately the same amount of XP as a 20th-level character who had a +1 Level Adjustment to deal with. Except of course that with an XP penalty, it's actually a certain percentage of XP lost, rather than actually having a higher total XP than a normal 20th-level character; this is actually a bit more penalizing for some characters (such as magic item crafters), but then again, an XP penalty doesn't suddenly add several thousand XP to the amount required for a new level; an XP penalty only slightly increases the time/difficulty in reaching a new level, but it persists in slowing down progression all the time, rather than immediately putting the character 1 level or so behind in terms of XP needed.
So overall a Level Adjustment is more harsh generally, keep that in mind when judging XP penalties versus Level Adjustments. As a result, I used 30% as the switching number for my above examples, because a 25% XP penalty only slightly slows the character's advancement for a time, and if faction abilities are gained every few levels, then the XP penalty will be replaced with weaker but more appropriate and immediate Level Adjustment. So......in general, make sure that the benefits of faction abilities gained, by the point that they would convert their XP penalties to a +1 LA, will be worth slightly greater than a +1 Level Adjustment in potency (since I mentioned previously that joining a faction should be overall more boon than bane).
For another point of reference, I figure a +1 Level Adjustment to be worth roughly 8 feats in power, or at the least 6 feats in power. Example: Being 1 level behind as a Fighter, for instance, you lose out on roughly 6 HP (5.5 avg; similar to 2 Toughness feats, though Toughness is a weak feat), +1 BAB (similar to 2 Weapon Focus feats, such as one melee weapon and one ranged weapon, though BAB is actually more potent than that for full-fledged warrior-types), +1 Fort. or +1 Ref./Will (roughly half a feat in equivalence generally), 2 skill points (roughly like a feat), and usually also a bonus feat, while an actual new hit die would also make the character harder to affect with certain spells and effects and thus has its own minor merits. So around 7 feats, but I know Fighters to be one of the weaker classes compared to clerics/druids/sorcerers/wizards, so I figure 8 feats or so to be a good estimate.
Thus for instance, if you decide to use my aforementioned possible conversion point of 30% XP penalty to +1 Level Adjustment, and let's assume a straightforward 10% XP penalty from each faction ability for simplicity's sake, then each faction ability should be worth around 2-3 feats worth of power after considering any non-XP drawbacks to the faction abilities.
Now then, as for the second idea I had suggested...... It would replace the XP-penalty-to-Level-Adjustment-conversion described above, and be simpler but still result in roughly the same thing, only a bit more staggered because it would more closely resemble Level Adjustments. This second idea would be to determine a specific amount of XP to act as a sink for each level at which a faction ability is gained...... This XP sink would be simply a sort of buffer between gaining levels, acting like a temporary Level Adjustment sort of deal. Meaning that as soon as they gain a faction ability, they immediately acquire an XP sink/debt/buffer of XYZ amount, to where any XP they earn beyond the amount needed for their next level is immediately lost to the XP sink, until that XP debt is paid in full, at which point any excess XP accumulated against that debt is then added normally to their actual total XP..... The character does not gain their next level until the XP debt is paid off, at which point that XP debt disappears, regardless of the fact that they do not start paying off the XP debt until their current XP already equals that needed for their next level.
This little peculiarity prevents the PC from being screwed if they suddenly die and lose a level or something from being Raised/Resurrected/whatever, since if they lose the level that granted them the faction ability, they suddenly lose that faction ability...... If they later regain that level at which the faction ability was acquired, then progress back up to the XP needed for the level following that......then their faction-based XP sink/debt remains in the same state as before, and once again prevents them from progressing further until they finish paying off the XP debt. (keep in mind that the loss of levels from dying and returning represents in the game a loss of memories and experiences, so it's fitting for them to thus lose their progress in understanding a faction's creed)
Besides being simpler, the second idea may also be easier to implement regarding stronger or weaker faction abilities, compared to the XP-penalty idea.
Let me provide some example now to better demonstrate this clearly....
Take an Athar for example...... Let's say that you set up the Athars to gain faction abilities at 2nd-level, 5th-level, 8th-level, 11th-level, 14th-level, 17th-level, and 20th-level, for a total of 7 Athar faction abilities. We'll say the PC Athar's name is Bob, for simplicity's sake. Bob joins the Athar in Sigil and, after a bit of preaching by the factors, comes to better understand the faction and agree more with their creed. At 2nd-level he gains the first Athar ability, let's call it Resist The Godslaves (I forget ATM what the Athar call priests...).
So Bob the Athar now has Resist The Godslaves, which let's say grants him a +5 bonus on saving throws against divine spells, but prevents him from worshipping deities or casting divine spells, and makes it such that he always counts as resisting any divine spell that allows him a saving throw (and any that Spell Resistance, if he has SR). Thus he must always attempt a saving throw if able, against any divine spell, and any Spell Resistance he may have will never be considered dropped or inactive when it could apply against a divine spell. This benefit is nearly equal to 5 feats, but its drawbacks and restriction to resisting divine spells reduces its usefulness to more like half that, at best, making it appropriate to the guidelines I mentioned before. The no-divine-casting restriction actually makes it even weaker, but only for characters who already had divine casting ability. In those cases you may want to add a stipulation that grants further benefits for those who give up divine spellcasting ability upon becoming an Athar. I don't recall at the moment if Athars could still be clerics or whatnot somehow, so maybe the aforementioned restrictions could be altered.
If using the XP-penalty method, then Resist The Godslaves may be worth a 5% or 10% XP penalty considering the 30% conversion point that I'm using as my baseline for now. If using the XP-sink method, then Resist The Godslaves, if gained at 2nd-level as I noted above for example purposes, would instead slap on a 2,000 XP debt for the character to pay off (I'm coming up with this number on the fly; it takes 1,000 XP to reach 2nd-level and 3,000 total XP for 3rd-level, meaning 2,000 XP inbetween, and I figure that the significance of Resist The Godslaves' benefits might be worth going from 2nd to 3rd-level twice as slowly as the rest of the party, and ending up 2,000 XP behind the rest of the party thereafter; it may be more like 1,000 or 1,5000 XP worthy, however, but this is just an example).
Supposing that you use the XP-sink method as noted above, then...... Bob the Athar just reached 2nd-level and gained Resist The Godslaves. He now has a 2,000-point XP debt to pay off later. He continues in his exploits about Sigil, and by the end of an encounter with some low-level clerics of Nerull that he and the rest of the party defeated, Bob the Athar finds that he has gone up to 3,250 XP after the encounter is said and done. The 250 extra XP is lost immediately however and goes towards his XP debt, reducing that to 1,750 XP in debt to pay off yet. And because of how the XP-sink method works, Bob the Athar does not gain 3rd-level yet, even though he has the normal total of 3,000 XP necessary for 3rd-level; he must needs pay off his remaining XP debt first, and meanwhile remains 2nd-level.
So Bob the Athar goes off and opposes some more stinking godslaves and furthers the Athar cause, and his friends don't care because they're fighting some plot by the priests of Nerull that would be really bad for the city anyway, and the party happens to be the good guys. Thus does Bob the Athar eventually pay off his XP debt after several more encounters, and at the end of one such encounter he finds that the encounter gave him 500 XP more than what he needed to finish paying off the XP debt; no matter, the extra 500 XP goes normally towards his total XP raising it to 3,500, and regardless, since he already had enough XP for 3rd-level, he now finally and truly gains his 3rd character level. He's payed off the XP debt from his first faction ability, so he no longer needs to worry about it, the first XP debt is gone for good and no longer bars him from gaining 3rd-level. Bob the Athar continues to fight the propoganda of the godslaves and continues gaining levels normally, at least until he gains another Athar faction ability, at which point he acquires a new XP debt to pay off, but as before it will only halt his progress for a bit.
Now, with all that said and done, you may want to make certain faction benefits into feats that have none of these aforementioned strings attached, because certain things the factions train for really do require the same amount of active training as would a feat or skill. Certain faction abilities you may feel better off making into skills, even. It all depends.
As for faction members leaving behind their faction or switching factions...... I think I'll leave that stuff for you to figure out, my post has gotten much too long already. Most likely such actions would eliminate any old faction abilities, old faction XP penalties, old faction Level Adjustments, or old faction XP debts that hadn't been paid off yet. Then the character would start fresh along the path of their new faction (if any), though perhaps they could receive some compensation for the lost progress and XP, up to you.
Oh, BTW, perhaps instead of specifying certain character levels for gaining benefits, you could specify a certain number of levels following the point at which the faction was joined. For instance, if a 5th-level character comes to Sigil and decides to join one the Athar, then using my previous example for them, instead of gaining their 1st Athar ability at the 2nd character level, they'd gain it instead at simply 1 level after entering the faction, and each additional faction ability 3 levels later than the previous ability. Thus, if 5th-level when they join the Athar, they'd gain the first Athar ability at 6th-level, and the second Athar ability at 9th-level, and so on, to use my earlier example for instance.
