Not sure if this is the suggestion box, but I have some, I think, simple modifications to help ease frustration and iron out some wrinkles.
-I would like to target my A.I. using the "F" keys like they are a P.C.
-Have the map open to Area by default and not the last panel is was on. Make the galaxy map center on player.
-Stop the A.I. from using healing abilities on turrets, drones, etc.
-Do not allow friendly weapon platforms to be targeted when cycling friendly targets. For example, ship mines, turrets, shield/health generators, etc.
-Be able to set the Tricorder/ship sensors to not detect anomalies, so they will only show mission objectives.
My own personal frustrating oddity is the rifle weapons stick out the back of my characters because the but stocks are too big. If I make a giant ape of a character this is not a problem, but for average sized characters it looks awful. Not sure if the weapons can be scaled to character size or not. Well that's my two cents of input.