Here are a few things which Bioware should add to the game in terms of plot/missions that would tie up some loose ends:

1) Hallow Voice: make this Esh-Kha an acquirable comp through an Alliance Alert. He and his followers were supposedly given a place to settle their kind at th end of consular story but nothing further was heard

2) SCORPIO: not my favorite comp but she's still a class comp for Imperial Agent. It would make sense to have the option to bring her back somehow if you chose to spare her, especially considering she can re-materialize into a new body if she wants (I.e. KOTFE ch 15 where she pretended to die but just took over the network and re-materialized on the throne). She could transfer some copy or part of her consciousness back into a shell to work for the Alliance

3) Darth Jadus: nothing about what happens to him after chapter 1 of the Imp Agent story but during the traitor/fractured alliances arc, Lana Beniko mentions this rogue Sith Lord as a possible suspect for sabotaging the Alliance, which means at least that he's still at-large with his followers somewhere.

4) Lord Vivicar: again, wasted potential with this character from consular chapter 1. Have a follow-up or even Alliance Alert mission to meet or recruit him or at least have him turn up again somehow in the future plot.