My picks:
Orcs and Goblinoids (and Xvarts): I can see orcs & goblins staying seperate, distinct monsters. However, I'd like to see hobgoblins & bugbears be retooled a bit: perhaps hobgoblins could be a orc/goblin mix (maybe with a dash of human), while bugbears could have additional traces (perhaps a bit of ogre), or could be magically-augmented hobgoblins. Perhaps merge the blue goblins & xvarts into one race.
Kobolds and Troglodytes: Perhaps make these guys one race--kobolds could be the younger offspring or weaker breed, with trogs being the older/stronger breed & leaders. Make it a sort of relationship akin to the dark stalkers/dark creepers.
Gnomes: I like gnomes, but I don't like them being a seperate race while being called "cousins to the dwarves." Perhaps make gnomes a dwarf subrace, or have gnomes be a halfling/dwarf hybrid that bred into their own race.
Dragons: Another favorite of mine, but the sheer number of beasties can be unwieldly. Rather like/prefer the idea of dragons being any alignment (rather than a fixed one), and would like to see the number of dragons go down a bit: perhaps based on the type of breath weapon/energy/element affiliation instead (fire, cold, electricity, acid, & sonic). Maybe with some minor modifications for variations based on environment.
Giants & Titans: Same thing as with dragons. Maybe a "core" giant race, but with some minor modifications for variations based on environment. Titans could be an evolved/aged/epic version of giant.
Undead: All forms of undead should be a template. But, I also think the number of undead types should be reduced: maybe to skeleton, zombie, ghost/incorporeal (with shadow, spectre, and wraith as variants), ghoul (as well as ghast & wight), vampire, and preserved (lich, mummy, etc.).
Drow (& Duergar/Derro/Svirneblin): Make them an LA +0 race, with class substitution levels (or levels in a Paragon class) to allow for the more powerful/potent variety. Same with duergar & derro (who should be 1 race), and svirneblin. Or, OTOH, make them monstrous humanoids instead of just humanoids.
I'm sure there's more if I could think of them ATM, but that's all that comes to mind.