IMHO the best is to capture the high PQ planets first and by the way try to destroy every ship and starbase you can find. Don't bother with the low PQ planets, they are the last to fall. If I am in war with another race that is my strategy and very often they surrender after I've taken 70-80% of all of their planets.
Private Joker
If you don't want to keep your ship designs, I guess the easiest way would be to just delete the .shipclass and .shipcfg files from the folder GalCiv2/ships in the MyDocuments/MyGames directory every time before you start a new game.
I know this game play feature from good ol' Pax Imperia. I think it's a nice idea, but as the above posters stated it won't work properly. Unless ... you could just withdraw your troops from the planet after conquering it, thereby destroying all of the improvements. After that, if you don't have any Colony in this system but there is a suitable planet, go for that planet with a Colony ship. That would give the Colony ships a reason for existance i
I don't think Stardock releases a game with such tremendous memory leeks. I also have problems right now to play a game on a large map but that is due to my hardware, a 1.4MHz Laptop with 500MB of RAM. One round in a late game period takes up to one minute.
The problem is, it's very difficult to create AI so it does not react on a linear way to your offers and diplomacy skills. I think that is a weakness that can't be eliminated in the near future. As the one's posted above, just don't use this bug or use it and get rid of the fun od the game .