I think you're underplaying it. It's not Weapon Focus (longsword), it's Weapon Focus (anything I touch). It's not Dodge, it's Dodge (*everyone). It's not Toughness, it's "I Effectively Have One Larger Die Type, Oh And My Saves And Concentration Are Better Too" (I think that's a Mongoose feat). A flat ability bonus always gives more advantages than any individual feat could give you. This feat throws that on its head.
And when was the last time you saw anyone take WF, Dodge, or Toughness as anything other than a prerequisite feat? IA (Constitution) is Improved Toughness (an average feat) plus 1/2 Great Fortitude (half of a weak feat) plus 1/3 Skill Focus (Concentration) (one-third of a weak feat), making it good--great, even--but not, I think, overpowered. IA: Str, Wis, and Cha come out weaker than that, Int possibly on par, and Dex a bit better, but even IA: Dex would only come out around Shock Trooper or Divine Metamagic level, which are excellent feats but not actually broken.
I wouldn't care if it overshadowed some feats that aren't part of the CO build hivemind, but it combines the benefits of several feats. In the case of a spellcasting attribute, it's a bonus to every school of spellcasting. No matter what you think of the 3.5 nerfing of spell focus, that's eight feats. Throw in Extra Spell, which it effectively gives, and it's nine feats. It makes anyone that has to take those feats (as prereqs, perhaps) feel like a sucker, which is always a sign of a badly designed feat.
On the contrary, anyone having to take bad feats as prereqs is a sign of a badly designed PrC.

If you make a very powerful PrC, you shouldn't balance it by requiring Skill Focus (Basketweaving), you should balance it by making it balanced. Most casters will have better things to spend their feats on than Spell Focus and Extra Slot (unless they're going for Archmage or are specifically building to try to make their save DCs ridiculously high), so again, it's not invalidating nine top-tier feats, it's invalidating nine feats that are kinda sorta okay to take if you need them for prereqs or you don't need any other feats right now.
As for limiting it to all but the highest ability - I know that if this feat existed in a campaign I was playing in I would game my ability placement to take advantage of it. I buy a 15 and a 16, the 15 goes in my spellcasting stat, the 16 in Con or some other secondary but important stat. Come 3rd level my spellcasting stat goes to 17, then at 4th it goes up again.
Granted, if you're using point buy this becomes a lot better because you can do exactly that; I'm looking at this from the perspective of rolled stats, where you're less likely to have your highest two stats within one point of each other and where you're more likely to have a low score you'd want to shore up.
That's nowhere near enough. It's an untyped bonus to an attribute, something which affects so many core uses. Raising even one stat is a godsend. Either it should only raise those attributes for explicit functions (like skill checks) or it should be a typed bonus, something that doesn't stack with an enhancement bonus (if a lower level feat) or inherent bonus (if a higher level feat).
Good point; I hadn't considered the type of bonus. An enhancement bonus would work just fine for balance purposes, though since enhancement is usually associated with magic another type might make more sense.
Another point of comparison:
Wish is the most powerful (non-epic) spell in the game. You would have to cast Wish twice to get a +2 bonus to any attribute, pay a cost 10000 XP, and even then the bonus would be Inherent (not untyped) and could only get you a max bonus of +5 (this feat is unlimited).
I think this is the most overpowered feat I have ever seen suggested, excluding joke feats.
Or, looking at it another way, you're spending a feat slot to buy a
headband of intellect +2 or
gloves of dexterity +2 and so forth. You get about 700,000 gp over your career but only 7 feats, so would you rather give up one feat slot or 4000gp? The prereq, then, should probably be moved up to ECL 5+, where the cost of the
[item] of [attribute] +2 is less than half your WBL.