The top change 3e made to the D&D spell system...

[Li Shenron]

I'm not expert on previous editions rules, but everything mentioned so far in this thread is something I really like about 3.0

 

[Zappo]

Let me think: Making schools of magic meaningless in favour for balance ?

I think that's only a very, very recent change, and still debatable. Besides, I don't like that conjuration is getting good blast spells, but even if that trend continues, one school getting blast spells in place of evocation is hardly "making schools of magic meaningless".

 

[Geron Raveneye]

I really like the further tweaks that Monte Cook made in Arcana Unearthed, making the magic system not only smoother but more customizable and useable. Very sweet system that I would LOVE to see make it into regular D&D.

Jason

Then simply integrate it, it's really not much of a problem. The Magister class can be taken as it is, if you want something to replace the Wizard...or simply ascribe it to a certain race only, like the elves, as a transition phase between completely intuitive sorcerers and bookish wizards.