The surrender code really needs looking at. I've lost track of the number of times 2 empires have surrendered (A surrenders to X, then B surrenders to A), leaving one of them with a whole new empire.
Also, if you can talk to surrendered empires they will give you an outstanding amount of stuff for peace since they are faction power 0, then they die at the end of turn mark. They really should die immediately or at least not be available for diplomacy.
Would also be nice if the unit colors switched consistently. This affects dead empire units turning pirate also.