Nova weapon in the expansion
I hope that in the Sins upgrade, the Trade Order most powerful weapon of mass destruction, the Novalith cannon is as powerful as it should be, because right now it dosen't seem to do much, in my opinion any weapon that has the ability to send a massive ball of energy through phase space and hit your planet should at the least cause collateral damage to nearby orbital structures and ships in its path of destruction.
Another upgrade that I hope is comming is more balance between ships such as cruisers and frigates, no matter how powerful a frigate is there is no way that a tiny frigate even with shields can with stand no more than a few shots at best from the main guns of a average cruiser and a battleship should be able to blast to bits a whole pack of frigates whether they are missile or beams in no time flat!
Deeper gravity wells, enemy ships come out of phase space and they are already within bombardment range of your planet. We need more powerful orbital weapons platforms or battlestations with anti strike ship guns.
Ability to target specific hardpoints on ships and or other orbital structures such as engines or sheild generators and more eye candy graphics.
More specific commands for ships such as protect capital ships and evade incomming missiles etc.
New purpose built warships for the Trade Order, for example the Kol is a purpose built warship not a civilian convert and by now the Tec should now be on a more war time footing.