Merciorum
Prince
Puppeted cities yield 50% less culture and science as of Gods and Kings.
I don't think it's in any of the patch notes (so take this with a grain of salt), but I believe puppeted cities get -25% to culture and science, plus some other disadvantages.
See this thread for a little discussion: http://forums.civfanatics.com/showthread.php?t=467577
Well. I need to go and do some stuff on my Egyptian game now . Thank you.