I'd like to see fewer classes, PrCs in particular, but I'd like fewer core classes, too.
I like customization of character abilities to character concept as much as anybody else, but this is just getting crazy.
Instead, what I'd like to see are more feats - both a larger list of feats and each character possessing more feats. Say you have the Wizard class. You could make him into the equivelent of a sorcerer or bard via feats for spontanious casting or magical music. The Cleric could be made into a Druid by taking feats that allowed wildshaping, etc... Fighter could be made into Paladin/Barbarian/Ranger equivelents via the same method. Or you could make some sort of wacky combination.
edit: I like Henry's ideas for classes. They jive with mine and take less room to type.
I guess it boils down to making most class abilities into feats and removing the multiplicitiy of classes/PrCs. This would allow for even greater customization of characters. The downside is the amount of testing it would have to endure to make sure there aren't any weird feat combos that unbalance the game, like what happens now if you mix feats from different sources.
I'd also like to see real, honest-to-goodness, set in stone RULES FOR MAGIC ITEM CREATION. Not guidelines. Real, core rules. I want all the items in the DMG to be made with this method. I want it to be sleek, efficient, and immune to power-gaming idiocies. I don't want to see another thread in the House Rules forum with somebody trying to make a ring of True Strike for a few measly thousand gold so they can get +20 on every single attack they every make ("it's only a first level spell, so it shouldn't be unbalanced....") Once these rules are set, put them in the freakin' PH instead of the DMG so the players can see what their craft-item feats can do. Charts for scroll and potion creation are, at the very least, a must-have.
Stats for summonable monsters need to be in the PH. Heck, a description of the Leadership feat needs to be in the PH. The PH needs to stand on its own - a player shouldn't ever need to even think about looking in another book.
I want Epic rules, but I don't want them to be called Epic. I just want them to be part of the game. Like the chart in 3.5 for taking the character beyond 20th, but better fleshed out. Spellcasting beyond 9th level (please don't call it Epic Spellcasting) needs to be revamped. Don't make epic feats, but make feat chains that are so long, they could take 30 character levels to complete.
Get those guys at Code Monkey Publishing to finish a character generator/editor/4.0 Etools
before the game ships. Put a demo in the PH just like before, but have a real product ready to buy if folks like the demo. E-Tools could have made so much money if it had been ready and working when 3.0 came out; instead, with all the mishaps and setbacks, it survived only as a niche community.
More monsters! I know there's a certain profit incentive to separate out the monster books and sell them singly, but I'd just LOVE a fat tome, combining MM1, MM2, FF, ELH monsters, etc... Templates for all undead.