I think Diplomatic Cruisers should be "Heavy Cruisers" (which, in naval parlance, is one above "Light Cruiser" and one below "Battle Cruiser"); they should be more impressive then any Cruiser in the game, but less impressive then a Capital Ship. You want to impress people with your fleet.
I would like to see sabatoge and treason in some form in the game, including ships suddenly being damaged when you attack the system they are in (sabatours detonating small bombs, or even a debuff to speed or weapons as the sabatour hinders them) and even some ships turn on their player when faced with overwhemling numbers AND overwhemling culture.
Moons. Seriously, please add Moons.
Artifact and Bonus frequency settings (I'd like to play an artifact heavy game).
More bonuses and Artifacts.
Capital Ships = Diplomatic Leverage... kinda hard to argue with someone when they have a Battleship in orbit of your planet armed with nuclear warheads.
New planet types (Jungle, Water World, Toxic)
Upgrades for planets that increase their ability to resist Espionage and Sabotage (just like fallout shelters are an upgrade). Also, upgrades for ships so they can do the same (such as loyalty indoctrination, maybe even hypno-indoctrination and even brain implants, each depending on the faction).
Are we ever going to see the race the Vasari are running from... in a game about Diplomacy, that would be the single greatest motivator of a triple unholy allaince. It would also be fun to have a fourth race. Okay, this is a bit much for a $10 mini-expansion, but maybe in a later "big" expansion? Please?