Have science automatically developed based on focus area.  Keep the four main  Science groups of military, science, etc. etc. have a civilization organically develop tech based on who they're connected with where they are in the galaxy.   


  At first, the tree is very narrow. The civilizations have a  few random techs.  As they connect with more civilizations and their population changes, gives them access to different ideas. It's a way of making the game harder without straight up making that AI cheat.  It also allows you  unique play throughs every time.  Maybe, just have it on the harder difficulties.