Re: BAB and saves:
I'd rather leave those alone for now, and leave the class-CR-exp-feats system alone, as they're mostly combat-based and taking on too much risks throwing the whole system out of whack. I'd rather fiddle with skills-as-skills, leave the rest, and if it works out well, have the experience with that to backwards-apply to the crunchier stuff.
Besides, a skill-based system probably raises skills far faster than the standard method (especially considering how often players make attack rolls for "real benefits"), and while that's not as much of a hassle re: most skills, the division of BAB, damage, HP, AC, attacks, and so on is something I'd rather not have to entirely redo.