Probably the number one thing I don't like about D&D is the way spells are handled.
Arcana Unearthed has a much better way of handling classic D&D magic: everyone is a spontaneous caster, and spells and spells slots can be manipulated (I can combine lower level spell slots to cast a higher level spell. I can break apart higher levels spell slots to cast more lower level spells. I can blow two spell slots when casting a spell to do something else with that spell, such as make it permanent or affect the damage or create an additional effect of some kind, plus more). There is no divine/arcane divide, and some of the 'game breaking' spells are either gone, changed, or much harder to get. (Ressurection, for example, has to be cast seven times over seven days on a corpse).
I think some of those ideas need to go further. There's simply no need for the sheer number of spells we have now. Having people 'build' spells on the fly is probably not the answer: it takes too long and you can also kiss any hope of game balance goodbye.
I like the way arcane powers are done in Blue Rose/True20 a lot better, but that's probably going a bit too far as well. I'd like some means of having a vastly smaller number of spells, then using feats, skill rolls, or some other mechanic to manipulate a base spell to do something else. Or similarly, spells that scale as you level. Cast Fireball as a third level spell, and you get n dice of damage. Cast it as a fifth level spell and you get more range, or a better radius, or something. Or use spell templates on it that change it's energy type, or make it subdual damage instead, or.. whatever. That way we'd need a much smaller number of spells (under thirty would be my guess) and never have a need for something like Spell Compendium.