That sounds like a good compromise solution, having smaller "waves" of fascist uprisings.
The pirates almost took over Japan?
My last game was as them, I guess I'll have to look out for bucaneers in this next version.
The fluid alliance system shounds very interesting as well. Can't wait for the next version.
EDIT: oh, and one more thing. I was looking at the screenshots you posted (they wouldn't load for me before) and I was wondering
if you could change the color of the Byzantines. That green is absolutely hideous! Either edit in a puprly color or even if you just switched colors between them and the Ottomans. I think switching the Green/Red would be more appropriate for those countries anyway.