Do forgive me if these suggestions have already been made, I just came upon this thread. Two things regarding companions:
1. Once you reach full affection with them you really have no interaction with them at all. I know extra conversations aren't exactly a 'papercut' (especially given all that goes into creating them), but down the line it might be nice to see something like a rotating daily conversation between you and one of the companions. Have the BH go on a hunting trip with Torian, the Agent visit the Killik hive with Vector, maybe the Trooper take everyone out bar hopping for some R&R. Even if this did become a bit repetitive after time (like all dailies inevitably do) you would still get the chance to interact with them rather than have them as window dressing on the ship.
2. The Jedi ship needs crew quarters. Every other ship has quarters where your companions presumably sleep. With the Knight/Consular ship all there is besides your own quarters is a bed in the medical bay and some couches. I'm not sure how exactly this could be remedied because re-arranging the ship itself to accommodate additional sleeping quarters doesn't seem practical, but perhaps the Jedi Council, taking note of the fact that the ship they gave you has limited space and you now have a crew, could give you an entirely new ship once you hit 50.