One game mode that still stands out for me as being very unbalanced is malfunction. The main reason being that the only way to track a shunted AI is with the captain's pinpointer, of which there is only one of on the entire station. This means that if it ever gets misplaced or given to an SSD person, the crew has no way of winning at all.
If you ask me, it's hard enough for the crew to break into the satellite and kill the AI as it is, and shunting just seems like a cheap way to deny the crew a victory and play hide and seek rather than make the round interesting.
Perhaps new ways to track a shunted AI would make things more fair. Maybe the robotics console or even the communications console on the bridge would allow you to trace the AI's self-destruct code signal. That way the captain or command could then relay that information to engineering to destroy that specific APC.
I feel like shunting in general should really feel like a "last resort" move that really gimps the AI's power in return for a few final moments of safety, like if there's only 60 seconds left for the AI to trigger the self-destruct, rather than a super hard to find and cheap tactic that screws over everyone, even when the AI has over 10 minutes left to blow up station.