I think the main thing as pointed out is that in seeking balance a lot of 'fun' or 'interesting' elements have to be thrown out.
This makes sense, as mastery of the Weave grants powers that are physically impossible to perform within the world's natural laws.
Magic by definition is bending/breaking the rules of the universe, and as such it should feel like it if you spend the countless hours needed to master it and persevere to the end. It took me dozens of hours of reading the spell descriptions from scrolls to just understand how spells interacted and worked together. It would have been far easier to say "screw it" and go with a fighter or paladin that focuses on disrupting enemy magic users. But I stuck with it, and am glad I did because using the magic system in BG2 is immensely satisfying. It requires an absurd amount of knowledge and expertise. It rewards future time orientation, patience and planning over impulsive "give me whats best right now".
Fighter and wizard wouldn't be very different if they were equally as effective from level 1 to level cap. They'd just be the same class with different variations of the same skills...which is exactly what happened in WoW.
Furthermore, unless you're soloing BG2, you have a party of six consisting of a variety of classes. Therefore, you'd never have to re-roll as a mage, because there would be a mage in your party ready to make up for any magical shortcomings you may have as a fighter. Your role then becomes keeping him safe and taking care of the less magically inclined enemies.
The MMOification I mentioned also has this issue of only allowing you the control of one character. This means all characters must be jack-of-all-trades, because otherwise someone will have to be stuck doing the less sexy roles such as tanking, healing or buffing/debuffing. Or in the case of the BG2 wizard, being completely useless for half the game.
Multiplayer game design has a long way to go before it reaches the wonders achieved in the past decade in single player games.
EDIT: I forgot to mention that enemy wizards also turn all of your strengths against you, because the player does not have any particularly special powers that enemies are denied. In fact, the player is at a far lower level for most of the game than enemies encountered and must rely on wits alone to survive most fights. There's a mod (Sword Coast Stratagems) that enhances enemy AI, and it is universally acclaimed as making BG2 into one of the most difficult games in existence. Every fight becomes a high stakes chess match...one small mistake leads to instant death. Aside from Dark/Demon Souls, I don't know of any games that come close to this level of tactical difficulty. I find these experiences to be immensely rewarding, and have a hard time playing mainstream games because they seriously lack this element.
But again, the fact that they allow you so much freedom in creating your character is incredible. You can even triple class! I sincerely miss this kind of freedom combined with the incredible depth of the AD&D 2nd ed rules.
I'm looking forward to Pillars of Eternity, but I'm quite sure that mechanically it won't be nearly as fun as BG2. Those developers just know better than to implement such insane mechanics again. Which is why it won't be nearly as entertaining.