Babylon + Korea
I'll take the science advantage over military any day.
Japan + Mongolia = ridiculous keshiks with generals and samurai city-takers. rape and pillage indeed.
In reality, I think it'd be best if you chose two civs that had UUs at the same time. China + Japan would dominate the medieval era. The Cho-Ku-Nos + the samarai would be almost unstoppable. Furthermore, the samurai would crank out GGs while the Chinese UA would make those GGs more effective.