I think it'd be nice if ships had two seats, one for the pilot and one for a co-pilot. The main pilot seat for each ship would be the one already in the game, and the co-pilot seat would be next to it, behind it, a different bridge console, whatever. How this works is that NPCs can control the ship from the co-pilot seat, but the main pilot seat is always kept empty for the player - when the player is in the main pilot seat, the NPC no longer has any control of the ship. This could have some benefits over the current system:
- NPCs can quickly take control of the ship when you stand up, instead of having to walk from the transporter room
- Less frequent silly moments like shoving your captain out of the way when you want to sit down, or having them trying to awkwardly shuffle past you when you stand up
- A bit of atmospheric fun of having a co-pilot in the cockpit with you