The problem with familiar-granted magic resistance is that you have to have your familiar within 10 feet, and the familiars in question have 7-10 hit points and poor saves. The first time you use that magic resistance against an area attack, you're apt to lose it. Better make sure you've got plenty of find familiar components on hand. (The incense is less of a problem than the need to tote around a brass brazier and spend 1 hour re-casting the spell.)
All familiars are Tiny creatures. If you've got your familiar tucked in your shirt, peeking out of your pouch or basically hiding anywhere on your person, the DM probably won't consider it a target for attacks (unless the opponent is specifically trying to attack the familiar, in which case I expect cover and/or concealment rules would apply).
Otherwise, most area attack spells would get rid of basically any and all familiars in their area of effect (average damage for a basic fireball is 28 points of fire damage (8d6) on a failed save, or 14 points on a successful save -- of all familiars, only an imp would survive that, and even then only because it has immunity to fire damage).
I do think it's intended that you should get the resistance; remember that the Monster Manual was released after the PHB. Because the sidebars just happened to all be on monsters that warlocks can get as familiars, I suspect the sidebars were a kind of stealth errata to beef up the Pact of the Chain.
That would be a
very strange case of errata, particularly considering that sprites don't offer magic resistance (and they're on special familiar list), and don't have the familiar sidebar in the MM, meaning that they don't offer even the improved telepathy all other improved familiars do (if you opt for that kind of reading of the rules).
Warlock's pact boons doesn't end when you get them, we also have consider how the pacts scale thru levels so we have to consider the available warlock invocations.
Among the three, the Chain pact is the pact with the least useful invocations to upgrade it thru higher levels. Leaving you with just an optional invisible familiar that will never improve its statistics or abilities. Easily the Blade and Book have it better thru levels.
Much as this entire discussion, that's entirely subjective.
If you take the blade pact, and
don't take thirsting blade and/or life drinker, is your character significantly weaker than he would otherwise be? I'd be inclined to argue so (albeit cautiously, since I haven't really looked into this). The 'core' warlock, a weak (at best) melee class
needs these two invocations to at least attempt to be good at melee. Otherwise his one melee attack per round won't make much of a difference... If you follow this logic, you could argue that the blade pact is the weakest of the three, as it practically requires you to take related invocations to make the full use of your character.
Also consider that in order to make the best use of this pact boon and it's invocations, you have to build your warlock differently than for other two pact; i.e. you need to invest in Str and/or Dex, and likely Con as well. If the game allows feats, you'll also want to invest in one or two of the armour-improving feats as well, since you're going for a melee-oriented character.
Tome pact is a bit trickier. Cantrips are nice, but are just cantrips, and are pretty much balanced against each other (e.g.
vicious mockery might be the only cantrip that deals psychic damage, but it uses a low damage die, d4, and allows for a Wisdom save). Besides, warlocks already get
eldritch blast, one of best cantrips in the game (force damage, d10 damage, multiple attacks).
There are currently 32 ritual spells in the PH, and virtually all are utility spells, i.e. nice to have, but likely won't break the adventure. Other classes get access to a lot of rituals (wizards get 17 on their class list, cleric and druid 14 each, and bard gets 12 -- all of those classes get ritual casting as class feature). The warlock has the
potential to learn all 32 rituals, but how many will actually be available to him through his gaming career is another matter entirely, particularly rituals from classes that don't normally write their spells down (i.e. any class other than wizard).
Also, unlike the blade pact, tome pact warlock does not require the pact-improvement invocation to be effective. Tome pact warlock without it will be fully effective during adventures even if he picks any other invocation; ancient secrets invocation will just give him more options.
Going back to the chain pact. If you allow MM sidebar rules for warlock familiars, Voice of the Chain master is practically useless to any warlock with imp or quasit familiars. Their telepathic link is already increased to 1 mile radius (as opposed to 100 ft. normal familiars get), which is likely more than you'll ever need, and since both imp and quasit familiars can speak and you're telepathically linked, you can just tell them what to say. Pseudodragon is a bit trickier, since it can't actually
speak, but it can communicate telepathically in a somewhat limited fashion. Sprite gets the short end of the stick. Again. I suppose it's just not special enough...

Chains of Carceri is, again, mostly flavour. Useful, but not required.
Chain pact main feature is to give you access to
find familiar spell, something only wizards normally get. If the wizard opts to get a familiar, the basic one (from the spell description) is the only one he can count one. Basic familiar is
not a sub-par option. Besides the wizard, the only other class that can have a familiar is the tome pact warlock who also takes the Book of Ancient Secrets invocation, and he also only gets the basic familiars.
Then, on top of that you get to pick from an expanded list of familiars -- something the class that the spell was designed for doesn't get. These improved familiars are already (mechanically) better than those the spell normally offers (invisibility, Stealth bonuses, shape change, spell-like abilities, etc.).
On top of that, they can attack (ordinary familiars don't get that option) using their master's action. While this will mean less at higher levels, it's fairly good at low levels, since all special familiars get special attacks (poison).
Besides the fact that the magic resistance of these familiars as stated in MM (IMHO), it may seem its a bit advantageous at the first few levels, but chain related invocations or familiars of warlocks will not scale or improve thru levels compared to Blade and Tome. It makes sense why these options were presented in MM.
Pact boon is a feature. It, by itself, doesn't offer a great boon. It's more flavour-oriented. You don't have to build a melee-centered warlock to use pact of the blade. If you focus on
eldritch blast and use pact blade only for its 'cool' appearing/disappearing weapon effect, you're not losing much. Compared to that, magic resistance is
always useful, regardless of level, regardless of your other class choices. As long as your familiar is there with you (which, traditionally, wasn't much of a problem in the game) you get it. No other class gets it (certain classes offer a similar -- but weaker -- ability, like abjurer at
14th level (and in reply to sithramir, paladins don't get it; Oath of the Ancients paladins get damage resistance from spells at level 7, but that's not magic resistance)).
Magic resistance gives you advantage on all saves against spells or other magical effects. You will
never have disadvantage on such saves, ever. This alone is a powerful ability. When you line it with the various warlock pact boons, it so clearly outshines everything else, even the main benefit of the chain pact (additional familiar choices) that I cannot imagine how anyone could expect it to be readily available at 3rd level.
Hmph. I've managed to write a novel here (even if it's a pretty boring one). I think I've managed to say everything I had on the subject

I suppose we cold agree to disagree on this one
Besides, from what I understand, there's to be a PH errata soon enough, so we'll see if the designers offer a clarification on the matter
Regards!