A quick comment on combat, specifically the number of NPCs you fight either on ground or in space. Aside from the obvious implication that our characters are supposed to be some kind of uber hero, it is not realistic that we should be able to defeat entire squadrons of ships or soldiers with our single ship or away team.
If you want to have a big battle, thats fine. But for it to be realistic you have to have friendly NPCs helping the player. If having friendly NPCs helping the player doesnt make sense for the story of the mission, then neither does having a huge battle. As uber as Kirk or Picard were, they never defeated entire armies by themselves.