I disliked a few things:
The game never explains how the Trandoshans took over the RAS Prosecutor or when the ship was attacked. All they said was that the Prosecutor was "lost" 2 weeks ago. "Lost" could mean that she went out of comms range.
The squad leaving behind Sev flabbergasted me. Why couldn't they take a short "detour" on the way to the gunship to see if they could at least try and save him?
I also didn't understand why the regular clone troopers were made so weak.