1.Single player campaign.
2.boarding actions.
3.pirates try to capture valuable ships(such as capital ships) and Auction them off.
4.some sort of "empire points"-players can earn more points by expand thier empire(maybe based on total population).and can spend them on something like megacapship,fleetcapstructure etc etc....
,big empires should have significant advantages now.
5.megacapship that futher increase the differences between races and provide support to fleet,for example:
TEC:a mobile fortress can build small ships and funtion like a commandcenter(hit chance,damage etc...)
Advent:spread culture everywhere(dont forget shield mitigation),nasty psi buff and big hanger.
Vasari:a phase stabilizer that can move,also can instill fear upon the enemy and damp thier culture.
6.more unique smallships.
7.ability to raise militia(cant phasejump): player can raise more "stages"(same as infrastructure) of militia depend on population of the planet,and need upkeep(so no turtle),for emergency situations only.
8.moons around the planet:though most moons are just small astroids,a moon has the quaility of the lunar would be very rare,but provide both big tatical and logistic adventages(even can be colonized).
9.gasgiant usually has many moons around them,essentially make them important strategy point.
10.even more easy to use empire tree.
11.winning conditions,so a game wont take too long.
12.maybe new unique races(think Dawn of War).
13.balanced superweapons and end-game tech.
14.Kamikaze,fireship,boarding parties,mind controls, add chaos to the battle.
15.enchanced diplomacy.
16.more anomalies,space isnt that quiet.
17.minor races?
hope this useful...