Crazy Awesome: The mod community qualifies for this by now. After seven years, and a ton of awesome ships, including the Federation ships from Trek XI. Including the ones seen so briefly when the Federation Fleet goes to warp.
Moral Event Horizon: Legate Matan is a slippery Manipulative Bastard who turned the otherwise peaceful Kessok against the Federation and has them construct House Arterius a massive fleet to fight for him. However, he loses all sympathy when he plans to destroy a sun to wipe out a helpless Kessok colony as well as all of his troops currently attacking it.
Player Punch: The destruction of the U.S.S Dauntless. Watching your old command be destroyed, even with all of the crew evacuated, is a terrible experience.
The Scrappy: Your First Officer, is universally despised among the fandom. One of the first things that happens in-game is you are given your own first officer, Saffi Larson. She never shuts up, and is after your commandplain as day. There are numerous mods ranging from "Saffi be silent" to Saffi is the first to die when the ship gets hit by anything larger than a cornflake. A mod exists also that replaces her entirely, though it's still in beta.
Scrappy Mechanic: Hitting an allied starship more than three times in a single mission will cause an instant game over. This is made all the more annoying by the fact that the AI-controlled allies are only too happy to wander into your firing arc... and the fact that the person who removes you from command is Saffi.