Optionally, only allow a class change every third level (3,6,9,etc).
Certain class combinations can be used to simulate other base D&D classes:
Fighter + Cleric = Paladin
Rogue + Cleric = Bard
As an additional option, characters do not get the +3 bonus to the specialty skill of that class, only the first class a character takes receives this bonus. This should cut down on min/maxing and allow characters to branch into multiple classes freely.