Hey, so where can I bitch about D&D game balance given that D&D message boards are full of idiots and assholes? Oh right I have a Livejournal, I can just bitch about any damn thing I feel like.
Yeah, so. Fighters and wizards. Or, more broadly, non-casters and casters. Pathfinder doesn't balance them. Someone asked "what would it take to balance them?" Basically I can think of two routes that make any sense and both of them are exemplified by games I don't really like as much as 3.5 or Pathfinder.
The basic problem you have is that fighters start out hitting things until they fall down, and wizards start out shooting things with fire or lasers until they fall down. As they level, fighters continue to hit things until they fall down, and wizards get to Plane Shift, create infinite wealth, stop time, teleport, divine the future, and also, if they feel like it, shoot things with fire or lasers until they fall down. This much is pretty straightforward and common knowledge; there's even a TVTropes entry for it to which I refuse to link.
The first approach to fixing it is the D&D Fourth Edition method, which I've heard a lot of derogatory terms for but basically amounts to "make everyone play the same game". This doesn't mean everyone plays the same, but everyone is working from a common vocabulary of damage, pushes, pulls, slides, shifts, stuns, surges and so on, with each class getting a few exceptional variants. You can build quite a variety of classes that play with very different feels this way, and you can balance them because everyone is playing the same game. The down side: nobody gets extremely wacky and bizarre abilities, because they don't model well within that vocabulary.
The second approach is the Tome approach, exemplified by the "Tome" homebrew set for D&D 3E created by Frank Trollman and "K". There's a lot of things I don't like about Tome; there's a weird cult of personality around it, for one thing, and they have some assumptions about how gameworlds should work that I don't like. That said, they have some quite sensible design principles, one of which is "If Guy A's schtick is 'hit things until they die' and Guy B's schtick is 'do everything', Guy A should at least be extremely good at killing things." The Tome approach is to turn fighters up to 11. A Tome fighter does not get magical powers, and instead gets the raw combat power to rip apart the monsters that terrify even archmages - in theory, at least. This leads to big numbers on fighters. Unsettlingly big numbers. That said, it takes a lot of killing power to counterbalance the power to just change the dang rules.
So there are the two options for fixing wizard vs. fighter. Honestly, like I said I don't like either of them as much as Pathfinder, although I think I like the Tome approach a bit better. Personally I would moderate it a bit relative to Tome and nerf wizards somewhat in the process - the Tome guys seem to prefer to balance around "wizards should do their best to break the game" while my mentality is "wizards shouldn't have to go out of their way not to break the game", if that's a distinction that makes sense.