And then there were two...
Actually, I think that the generic expert can be done away with entirely. Just add a new feat, which can be taken multiple times, that adds 2 class skills and adds 2 skill points/level (quadrupled at first level as normal if this feat is taken at first character level).
Partially this was because I agreed that the Expert was underpowered (you can search for that rant using keywords "expert" and "shaft")

but also because I came to realize that their "niche" could be easily duplicated by feats that give skill points, as above. I mean, what does the expert "do" except have skill points? The warrior can fight, the spell-caster can cast spells, but since they all have access to full choices in class skills, the expert only has "more class skills, more skill points", and that is frankly not enough to hang a hat on.
Oddly enough, even with just the two generic classes, there is still a prestige class that might solve your partial spellcaster problems: Eldritch Knight. You get a great BAB, almost perfect spell progression, and at the cost of a drop-off in feats (only 1, instead of 1/five levels for spellcaster). I guess that brings it back to three classes again. For divine spellcasters, you can create the Carbon Copy Divine Knight (or just do what I do - smoosh the two spellcaster classes together and say that all spells are both divine and arcane, just to simplify things further -- I mean, the only real difference is two feats (turn undead, familiar) and armour spell check penalty (arcane). Unless someone thinks that having the potential to gain a familiar is wayyyy better than having the potential to turn undead, it seems like the divine spellcaster outclasses the arcane spellcaster when it comes to wearing armour, unless one does something. On the "spells are both divine and arcane" rule, armour hurts the spellcaster's chance of casting, but the spell caster can potentially both have a familiar and turn undead - oh, and the spellcaster can pick any of the three "mental stats" to be the relevant spellcasting stat).
So in total, I like the idea of going even MORE generic (one spellcaster not two, no expert) but then putting in a prestige class. This leaves us with warrior, spell-caster, and (possibly) Eldritch Knight.
Oh, I would also give the warrior access to Greater Weapon Focus, Weapon Specialization, and Greater Weapon Specialization, using the warrior levels instead of "fighter" levels (since there are no fighters). I also would extend those feats so that at 16th level the warrior could potentially get "Even Greater Weapon Focus" (+3 instead of +2) and at 20th level the warrior could get "Even Greater Weapon Specialization" (+6 instead of +4).