Is the lag persistent at all points of the game?  Or is it only in the late game?  Constant lag is probably, as Wrath pointed out, due to the network and not your computer...but if you are only lagging late game then it's probably a performance issue...

This may not be relevant at all, but out of curiosity where are you playing?  Like, are you just using your home internet or are you playing off of a buildings WiFi (work, or university for example)?

Well that is rather strange...beyond wild guesses I haven't a clue why that is...is it starbases in general or a certain faction's?

This is a complete shot in the dark, but iirc the advent sb got a lot of work in the sins optimization project....could be that sb just doesn't mix well with your computer....could try out the sinsoptimization project and see if that helps