In general I prefer 3.5, but here are the things I don't like (and house-ruled back to their 3.0 version in my game).
Nerfing Alchemy (Alchemists now have to be spellcasters, so no Expert NPC alchemists, or PC Rogues picking up Alchemy to make their own thunderstones/tanglefoot bags ect, they also dropped the 3.0 Alchemy rule that a DC 20 Alchemy check can ID a potion). Alchemy wasn't overpowered before, why weaken it?
Pokemounts. *shudder* I'll take Paladin Mount Classic thank you.
Buff Spell durations. I don't mind making them a flat +4, it's the shorter durations I don't like. I happen to like the idea of PC's using their spells to power up instead of being dependent on items.
Nerfing Polymorphs. The 3rd Edition Errata Polymorph Self/Other will do just fine. I really don't like the "Baleful Polymorph" nonsense, you can only turn them into a harmless tiny animal?
Weapon Size Rules. Questions of realism aside, it's just a hassle to keep track of most of the time. Yes, there can be Halfling-sized polearms and quarterstaves (but a quarterstaff for a small-sized creature would be a jo-stick for a medium sized creature, and be usable as a club IMHO, and a halfling-sized polearm would be a greataxe or longspear for a human)
Darkness is produces light, huh? I still use 3.0 Darkness effects in my games.
Bard as the Gnome favored class, say what? Since when were Gnomes renowned bards?
As for making the game more mini dependant, go ahead, but I'm not buying the WotC minis they made them for, too expensive. I'll stick to lego figures and my cheaper Mage Knight minis (yay for the 4-for-a-buck bin!), and all my old HeroQuest minis from way back when.
