Wow. I seem to be in a very strong minority of GMs here that use that house rule--and not just for ease-of-use, but because I think it should be that way! (Note that it's only permanent changes--via Wish, levelling up, etc. Items, spells, and other temporary changes do not count for skill point increases. --And, for the record, I disagree even that not changing skill points for temporary int changes is the way it 'should' be. I am just forced to do it that way because any other option is horribly complex and too easily abused.)
Part of my reasoning is balance between the stats is balance: 1) if you don't give skill points retro, then there is ZERO REASON for a non-mage to increase int. Period. End of story. A player would be stupid to do so. 2) it's the only stat that takes such a nasty hit to how it's used. Int is used (for non-mages) only for a) skill points per level, and b) bonus to int-based skills. That's it. We're done.
Let me argue against the common reasoning: that you can't suddenly learn new skills. Well, flavour text can be used to justify anything. And, when you come down to it, all that crap about "Well, you can't suddenly know a lot of stuff, but your body can suddenly be tougher" is nothing more than flavour text at its core. A mage gains a level, and suddenly has at least 6 skill points (usually) to distribute. RAW, he can put all six skill points into one skill. If he's level 2, that *exactly the same effect* as if he had somehow permanently increased his Int by two points. But one, simply because of the wording of flavour text, is allowed. The other is not.
Now let's look at Constitution. You see, Constitution is a measure of how tough your body is at any particular moment in time. Hit points are a measure of how your body develops over time. If hit points were not a measurement of development over time, then everyone would have their points based exclusively on constitution (or maybe constitution and class)--level would have nothing to do with it. But since levelling *always* increases your hit points, obviously hit points are a measure of development over time. Therefore, hit points should not be retroactive. You gained 7 hit points on reaching level 2; how did you 'suddenly', retroactively, gain one more hit point for that level? If anything, it's worse than that: wear a necklace, and you retroactively gained 1 (or more!) hit points for previous levels. Take it off, those bonus hit points are gone. Put in on, take it off, put it on... --You can die from this silliness!
So. Do you see why trying to justify a point via flavour is fruitless? Flavour text can justify anything. Sure, you can argue my reasoning about hit points--but the whole point of this is, my flavour text *sounds* like it makes perfect sense!
The reasoning for not giving retroactive skill points for (*permanent*) Int increases is arbitrary, not really justified for balance or common-sense reasons, and hoses anyone wanting to increase Int (including those poor mages).
So why not give it to players?