I am a GM and I love wizards.
When I talk about limiting wizard spells, it is because that is something the GM is permitted to do in order to steer the course of the campaign. It is also my favorite part about wizards, since you can really express a lot of flavor in the spellbooks if you so choose.
For instance, a wizard PC in my game can find that purchased conjuration spells are often written in a Korvosan syntax with a Chelish spell grammar, owing to the influence of the Korvosan Acadamae. "Elfy" type spells are similarly in an Elven syntax, and may be selected by me to line up with the history of elves in Varisia. I'll even allow extra spells to be deciphered from captured spellbooks along these lines (I used a Linguistics roll).
I've also allowed the flavor aspect of spellbooks to serve as a major clue in my Rise of the Runelords campaign. Without spoilering, I can say that a clear connection exists in the grammar of several captured spellbooks, which gives players information they mightn't ordinarily glean.
Sometimes I will limit the access to certain key spells because I just don't like how they feel for that campaign at that point. This isn't done to hobble the PC, but rather in service to the campaign. The Wizard list certainly does contain some of the greatest spells in the game, and sometimes as a GM you see it coming that it would hurt the experience overall. Sometimes, you go ahead and allow it anyway. If you're doing it to increase the overall fun for the PCs, you're doing it right.