A proper win condition.
Some plot-relevant use for the hypershunt, and one that does not involve planting Pather cells on (or otherwise harm) your colonies. Currently, hypershunt is only good for killing Omega ships and taking their weapons.
Recurring Omega fights that drop more Omega weapons. Does not have to be common like Ordos. Maybe one Tesseract per year if nothing else.
Better skill system than we have today. Meta today is mostly about Leadership, strong fleets, and missiles. Player is gimped without a Leadership capstone (or Ziggurat).
More recurring late-game enemies on par with Ordos and do not rely on shields. (i.e., have an Ordos caliber faction that use heavy armor and unique defenses, and no normal shields, so that kinetics is not the one damage type to rule them all.)
More - and better balanced - ships for Derelicts, give them at least as much variety as Remnants. Find another way to make Derelicts weak aside from small hulls not worth their DP weight. (Remnants are strong not because of their hulls, but because of excessive alpha core spam.) Bonus points if Guardian gets replaced for Derelicts by more appropriate ships and used only as the sleeper ship boss. (If Guardian stays with Derelicts, it needs to be rebalanced badly, and ideally recoverable for those with Automated Ships.)
Uniquify the player faction, with paintjob hulls and a unique ship or two his industries can build for his patrols and personal use, even if it has to be a conversion job like Pegasus->Executor. (Although it would be better if it was a unique design altogether.) Diktat seems relatively young like the player faction, why can't the player do it if his game lasts long enough? Five size 6 planets with strong economy and military is major faction strength.