Oh, where to start?
I agree the economics are screwy, but that's been true since Day 1 in D+D; I doubt it'll change, if only because people like seeing great big numbers in their g.p. column.
As a traditionalist, I'd like to see non-standard PC races come right out of core, and at most be a minor option in some expansion book. (and if DM's want them before then, they can always wing it)
Slow down level advancement. Or, have a dual-track advancement and ExP table - one track for short (1-2 year) campaigns and one for long (5+ year) campaigns.
Give DM's more latitude to tweak the game to suit their/their players' style. About the only way to do this is to make things a bit more modular, to remove some of the knock-on effects where changing one thing affects 12 other things, but this would be a nasty design challenge.
In general, bring back some of the notion that it's the DM's game. 1e is the DM's game all the way, 3e is much more the players' game; there's a good mid-point somewhere between.
Get away from the slavery to having linear progressions for everything. For example, I'd really like to see Bards' BAB go up quickly for the first few levels, then slow right down after that, and eventually stop. Ditto wizards; after about 10th level, why would they ever bother learning how to fight better?
Dont' be afraid to look back at earlier editions for good ideas to incorporate; System Shock Survival and Resurrection Survival are two examples.
Lanefan