Classes can be limiting in some respects. However, I feel that D20 has addressed this problem in many different ways:
(1) They always say..."If you don't like something, don't use it or change it." This is great for me as I have done some modifying of the D20 rules for D&D for my current campaign, making it exceptionally high powered (almost an Elric from White Wolf sort of difference between the heros and the "norms") but it is fun for the players and I like it too.
(2) Wizards has been relatively good about offering numerous variants that can be used if you don't like the standard rules. In Unearthed Arcana they even go away from the standard classes and offer the variant of "Generic Classes" that offer you a template of warrior, expert, or spell-caster, but allow you to customize a class in almost every single facet, from savings throws to feats, etc. And that is setting aside the "Gestalt Classes" which is even better than multiclassing as you go up in levels for 2 heroic classes at a time.
I feel that a class based system is great for balance, and, as long as the GM ensures balance among the Player's characters, any modifying of the classes is fine.