Just like one can choose the opponents for the starting sector. Why not add the ability to choose opponents for unexplored sectors. That way when one is able to go to different sectors they may be met by a surprise of an AI built up as much as them.
Like in Deep Space 9 the worm hole opened up a new sector and the Dominion was not happy.
Think of how this would help put new life into a game you thought you had won.