Hmmm.
I've used the Flaws a few times, the alternative rules for specialized casters, and the fractional BAB and saving throws.
I'm cool with Flaws - I like opening up another feat for my players. The alternative rules can be a bit powerful - I enjoyed playing a Conjurer who could summon as a Standard action instead of a full round, but it did feel like I was gaining a big advantage with it. On the other hand, it certainly encouraged me to summon like crazy.
The Fractional BAB/Saves was a bit fun to play with, but it got confusing at times and I had to keep re-checking my math. I like the idea in general, though.