I think Lysanya has a good point. Gunner should always be in slot 2 once the match starts, even if they are not that way in the lobby. Maybe an auto-switch when someone picks gunner. Anyone joining the match NOT in slot 2 would NOT be allowed to choose gunner. Ever.
Also, this would help.
With popup warnings that two gunners are NOT recommended, and hoverhint over the ! saying the same thing.
I would also suggest the following procedure:
Someone tries to join through match list.
Pilot sees "X is joining your match in 30 seconds."
Pilot can click something to see loadlout (can never be a second gunner) and can talk to the person joining.
Pilot can wait the 30 seconds, or accept right away. Scrubs may not have enough patience for 30 seconds, and leave.
AI does not vanish until the player actually interacts with something, or within another 30 seconds, instead of vanishing the instant a player moves. Player can access the toolchest (see below) without making AI vanish.
This set of events gives the player time to fully load in and assess the situation, as well as giving the pilot time to adjust for a new crew member without having to ask "What did you bring?".
Finally, on-ship tool swapping. This should be an actual 'Tool chest' location on the ship you have to go to, click to open, and change tools. It could only be done once per match (or per time limit), and a message would be sent in chat to the entire match. "Name has changed to SPANNER - MALLET - CHEM SPRAY - CHARGED"
Aside from trolls, this would make crew joining run much more smoothly.