Heres a list of things I dont like about D&D 3.X
The Magic System, I hate the whole spells per day thing
Confirming Crits
Levels/Hit Points
But Pathfinder seams soo well done and seams to have soo much love invested into it. The books seam worth the cost (unlike 4e IMHO) and the fact that they are on board with the OGL is awesome.
Because PF is an OGL-based game, the variants available within the OGL communitity can be applied pretty easily with the PFRPG. Specific to your points:
The Magic System - I moved on from vancian fire-and-forget magic systems 10+ years ago. All of the variants available for 3.x and OGL gaming could be adapted to PFRPG just as easily. Some of my favorites include:
The Thieves' World magic system. Magic casting is a roll. Characters get a spell progression for acquiring new spells. How often you can cast them is dictated by their ability to sustain fatigue (i.e. non-lethal damage).
True Sorcery - similar concept but allows for customized spell creation.
Elements of Magic - very flexible spell construction, magic point system
Arcana Evolved - Vancian done right. Not sure how to apply it to the various PF spell-casters, though.
Confirming crits - easy enough to house rule out. Wouldn't factor into my "worth it or not" decision criteria.
Levels/Hit Points - Levels, well those are hard-wired. Abandon that and you might as well pick something else. As for Hit Points, multiple options available: Vitality/Wounds, Reserve Points, Trailblazer tweaks, Damage Saves, etc.