I have to wonder, why was there no changes for spells included in the alpha release?
The single most gamebreaking elements of 3.5 were the spells and the druid. Two things that you've ignored in the alpha version. As far as making 3.5 better, I really doubt you can do that without fixing the spells.
The polymorph mechanics (starting with alter self) especially need a complete overhaul, as does planar binding, charm person and command undead. Hell, pretty much the entire 9th level list of spells with gate, astral projection and shapechange need to be looked at. You've also got a ton of fighter screw spells that should probably get toned down, like maze and forcecage.
We've known about these problematic spells for a long time. They really should be fixed.
