Greg K, Shades of Green and Ari pretty much covered most of my wants, but I'd like to emphasize learning from the various work that has been done in 3.0 and 3.5 what *isn't* working out.
For one example, Savage Species was a great look at how utterly messed up monsters were compared to PC races. The stats were just thrown down in the Monster Manual it seems, and once they started converting them, the strangeness got showcased. Turning into a graverobbing flesh-eating Ghoul probably shouldn't increase your Intelligence, Wisdom and Charisma by 8 points after all! (Hey, the King died and now walks around naked and hunched over, reeking of carrion, attacking anyone he sees and munching on human limbs, but he's even more regal and diplomatic than ever, and his Leadership score went up! He's so dreamy, I'm gonna introduce him to my sister!)
Most of the beasties should, IMO, be written up with an eye towards how they would fit their flavor text, as compared to the human baseline, not just given arbitrarily high (or low) stats. Dwarves, a heirarchical and organized race with lines of succession and famous kings and priests and leaders, for instance, don't make sense to have a lower than average Charisma, only half-breed races that have some rationale to have a racial inferiority complex (half-orcs, half-elves, half-giants), insect or hive mind creatures (aspis), cursed outcast creatures (driders), chaotic and / or mindless species incapable of functioning socially (many undead) or races that have another very real reason to have a racial inferiority complex (goblins, kobolds) would make sense to have a weak sense of self, and thus a racial penalty to Charisma. The Dwarf seems to have a Cha penalty purely as a 'dump stat,' not because Dwarves are inherently servile or anarchic.
The idea of racial levels and 'lesser races' and 'race paragons' creates a lot of possibility for customization, which I like. The idea of the immortal and physically fit elves being sickly and frail (but never fat or ugly!) never really fit for me, although I can see how it works for others, so I'd love to see an option that did away with that.
It really feels to me like the MM beasties and the PHB races followed completely different, and barely compatible, design guidelines. I'd like it to all come from one baseline.
In a fit of complete contrariness, I'd love to see bizarre stuff like the Spiked Chain ditched, in favor of 'normal' weapons, armor and equipment. Yeah, I get it, a world of fireball throwing wizards and flying multitonned frost-breathing white lizards, but there is a place where even *my* suspension of disbelief won't go, and the Spiked Chain is there.
As for the rest, the magic system, particularly the slots-per-day and metamagic systems, could use some tweaking, I'm sure, but heck if I'm smart enough to know how. Monte's Arcana Unearthed had some interesting ideas, with the modifications of spells on the fly by expending extra slots, or using slots of higher or lower levels.