First get rid of the mission system it is useless.
Then develop a system that allows the player to make demands, trading options, and diplomacy options with the computer players. Start the game with neutral attitudes with all computers, until first contact where you can meet the race and decide to go to war or continue to be neutral. Then from there you can communicate with computer players and offer traders or alliances, or simply free passage through each others systems. You could also demand territory or ships from weaker players, with the threat of war, or offer technology to bribe another player to attack a aggressor.
These upgrades would give the game a whole new depth, and give back the option of playing a open alliance game without all the computers ganking the player.
Those are some of my ideas for a good diplomacy system