I absolutely cannot stand it when other pilots quit because they want all engineers, or they don't want two gunners. If you want to try to run the perfect loadout with the perfect crew, join a tournament. For what amounts to a pick-up game at the public ball courts, get over yourself and just play the damn game.
If you're not willing to flex your ship for the crew and expect the crew to do all of the changing for a public game, you're a captain in slot selection only.
This is rather melodramatic. Like most of the veteran captains here, I am delighted to play with newer players who are eager to listen and learn. Players who ignore me or shout obscenities at me when I politely request that there are at least two engineers on the ship I don't really enjoy playing with. If a new player says "Can I play with this class/ship/loadout because I want to practice it and/or get the achievements?" I would be only too happy to oblige. It's the players who are obtuse and don't even attempt to constructively communicate why they're doing what they're doing I eventually give up on for a better crew.
Likewise, I once had a level one co-pilot who flew a squid, picked all mercuries and parked directly in front of a galleon's left broadside. This was a little frustrating and didn't work out too well. Still, he listened to me carefully when I explained to him a better strategy and loadout to try with the squid, and how to use it effectively with an ally, and we were winning matches in no time (by the way, this wasn't Gilder, as funny as that would be XD). I was really happy about this. If a co-pilot wants to ignore me or insult me when I'm trying to work with him and give him advice, however, I see little point in playing with them other than out of a perverse curiosity to see how badly they do.
If I'm engineering and a captain asks me to go with a certain loadout, then I'll respect it, even if I disagree, because it's his/her ship and they know how they want it to function. It's no fun for the captain if I just ignore him and go pilot/gunner when he wants me to buff and repair his engines and hull.
Just to summarize; communication is the key. It's fine if you want to play a second/third gunner, or an unconventional ship and loadout, but at least talk to the rest of your team about it first. If they're not ok with it, that's a shame, but there are plenty of other matches you can join.