From what I've heard, third edition was "balanced" based on the theory that fighters would be on the front line hitting enemies, rogues would be hiding in the shadows and making backstabs, clerics would be buffing/healing from the second rank and wizards would be casting offensive spells from the rear.

Unfortunately they left plenty of opportunities for the spellcasters to be far more creative with their offense. Clerics can become literal gods of war using the right combination of buffing spells. Wizards can pull off some combos that annihilate all in their path.

One of the core problems, aside from not enforcing class roles, is that all classes have the same "cost". When you get enough XP to gain a level you pick a class to level up as. Logical would dictate that all classes be equally valuable since the "cost" is the same. That simply isn't true. Early on wizards have strong limitations and a fighter is technically better but enough wizard levels ensures that battlefield dominance. In 2nd edition they fixed this by requiring different amounts of XP depending on your class. But 3rd edition went for a "unified" model for gaining levels. Changing back could help fix the problem a bit.

There are other things you do - make all persistent spells require concentration. So if the wizard gets hit they might lose their concentration on their mage armour spell for example. Some spells might require more than one round to cast.

4th edition has kind of fixed things, but that is by completely rewriting the system so that the differences between classes are mostly fluff. Everyone just has their own different batman style utility belt.