I know this has been suggested before, but it honestly deserves its own thread.
Every time a player joins a ship mid-match and replaces one of the AI, the AI disappears immediately. This wouldn't be a problem if it weren't for the 20-second or so loading time. That's 20 seconds where the crew is down one man. This makes enough of a difference to completely turn the tables in a match.
Please make it so that the AI stays until the player's done loading in.