I am curious about the future of the Lucrehulks in the first place. I know Zsinj will get them since CS was within his holdings, but does that mean PA will loose it?
Second in my list is the Vengeance. Since EaW does not handle the both space and ground hero at the same time idea, It might be best to separate Jerec and the Vengeance and give the ship to Captain Sysco. Since PA starts pretty strong with 2 SSD under it's command and having a relatively good starting position, I also say that the Vengeance to become "recruitable" where you would have to pay a huge amount of credit for it(even compared to other SSDs) but having an instabuild. So to speak you "fund" it to operate within the Alignment, but requires Jerec to be present in order to represent that it is his ship after all. This way even the AI would be able to use it properly.
The third and the most burning one in my opinion the remnant Hero rooster.
Since the Warlords will have their own factions, the IR will lose most of it's Era 3 heroes in the multi era GCs. In shadow hand it can stay as it is now since they seemingly worked together at the time, but in a multi Era GC it could bring troubles, like Teradoc and Delvardus being in two places at once.
Teren Rogriss could be one of the Candidates who could join the IR ranks, since he was with the remnant until at least 13 ABY, and he and the Agonizer are already in game in the Zsinj GCs.