Features could be added which might make the game more fun.
1) The option to specify starting location in center of map or edge of map. Game play changes quite dramatically if you start in center or at the edge. It would be nice to be able to request this rather than restarting till you get one or the other.
2) The ability to select if an particular AI opponent gets a 5, 10 , 15 or X turn turn head start. To mimic the condition of an "Older" established race for the larger map sizes.
3) Adding some stealth techs to minimize opponent sensors to some degree.
4) Modifying some .5 value trait factions skills. Currently some Trait faction skills just aren't worth the whole point such as sensors etc.
5) Upgrading ships further away from planets / starbase too cheap and easy. For example I can build a faster constructor, zoom it to your build spot and then upgrade it to a cheap slow double constructor at destination to get extra starbase build. All sorts of exploits base on this factor right now.
6) Repair modules for starbases, and having improved repair rates at the ship yards..
7) The ability for human or AI to fund or give pirates ships, Starbase, Ship Yards or funds to speed up pirate (think England funding of pirates to Harass Spain.)