It reminds me a lot of the design of Champions Online. You could mix and match just about anything you wanted. Gaining greater powers of a particular type only relied on greater investment within that power-category. IE: the best fighters are the ones who dig deep into the fighter tree. However, slight cross-polination was common, even to extremes it was common because it provided for very thematic(and effective) character creation. However, system mastery reigned supreme. The guys who could put together the right points here, the right powers there, were 1000000 times more powerful than anyone else.
I think the key here is to learn from 4e's "Hybrid Classing" system. Put a cap on how many classes you can take. Establish some form of loss for multiclassing as well as a gain. Taking a level in rogue after having a level in fighter may only net you half the stuff the guy who took rogue as their primary class got. The result of a fighter taking wizard levels should be different than a wizard taking fighter levels.
Yes agreed with the second paragraph. Also you have to be careful of stacking modifiers from different classes/class items.