I think most of what I miss has been covered, but here goes.
Settings and flavor - I, too, miss that feel from the 90s. Lots of good setting books in that time. I really wish I had the chance to play Al-Qadim! Some of the old-school flavor with wacky magic items would be great.
Alignment - Classic 9-alignment system for me, please. I find that the new alignment system doesn't work for me, especially since I play Dragonlance. I've house-ruled the classic alignments back in. Glad Charcter Builder is cool with house-ruled alignments.
THAC0 - Miss the term, not so much the rules. I liked the basics to BAB. I just wish they used the term THAC (minus the zero) just as a wink and nod to prior editions. That being said, I think THACO would make a good nickname for a tinker gnome.
Skills - I like some of the consolidation, as it makes a lot of sense. Stealth instead of hide and move silently is spot on. I always landed up rolling both together anyway. I think perception as a skill is awesome, as it allows for use of your other senses. Back in 2e, I had a character with an extreme sense of smell. That would have worked perfectly with that. However, I do miss some of the craft/knowledge/perform/profession skills. I'm trying to get to know backgrounds from PHB2 better to see if that truly covers it. Skills could really be in a middle ground between 3e and 4e for me.
Dragon and Dungeon in print - Ditto, me too.
3.5 psionics - Ditto, me too. Great system, one that went back to the flavor of 2e without the clunky rules problems. I don't know how they can recapture that flavor in 4e.
OGL - I can understand why WotC moved on from a business model, but the OGL brought us so many amazing products!
Racial Negatives - While it's simpler to add numbers, some races need to have negative modifiers! I keep going back to gully dwarves. How can you play a 4e gully dwarf without a negative to your INT score?
Ability score order - I have a hard time with Dex and Con being switched. lol
All of that being said, I'm having fun with 4e. Great system, and a lot of what I want can be ported back in.