[dogscoff]

I'd like to see the game's definition of an "empire" and the diplomatic model made more flexible to allow ideas like these to be included.

Each pirate fleet would be an "empire", even though it had no planets. That way you could try to buy them off using the diplomatic options, you could ally yourselves with them (and sic 'em on the enemy=-) and even conquer them. Tying it into the existing diplomatic optins like this would also simplify the interface for dealing with them.

Extra-galactic visitors could be handled in a similar way, the only change necessary in the code would be to allow spontaneous creation of new empires mid-game (this can already happen with planet rebellions, but that seems to be handled as a bit of an afterthought in se4.)
All you'd need to do is spontaneously create a new empire, hand them a few high-tech warships/ colonisers/ troop transports and then just let the game do what it already does.