While I don't have the time to contribute to this project, I do like following the progress of 3e revisions and I might comment from time to time. First comment: Finally, a revision that plans things out ahead of time!
So I'd suggest laying down a short list of bonus types to stick with and not deviate from them, same with damage types. Off the top of my head, I'd merge sacred and profane (they're thematically the same "from an aligned power" bonus and can cause edge cases for people who can get both), drop alchemical as a type (enhancement should cover alchemical items just fine), and fold dodge bonuses into circumstance bonuses (they're fiddly and stack with themselves, two things that aren't necessarily good design) to start with. I've found that breaking all bonuses into five types (competence from equipment, enhancement from magic, inherent from race, insight from class, and circumstance for other stuff) works pretty well, but cutting things down that far could be too much depending on your other design goals. As for damage types, the five element types plus two energy types plus force work for me, but that's up to you folks.