I have worked up a set of house rules designed to alter Pathfinder RPG to make it even more customizable and flexible, and to remove some aspects that I don't like. I'm getting too busy these days to be able to ever put it to use, but I figured I'd share it and open it up for other people to critique and use in their own games if they want.
Here is a google doc of the rules, I've enabled commenting. Please let me know if you see a mistake or something that doesn't make sense, etc. Thanks!
PFRPG Heroes Mod