Obviously the 5 min cool down I suggested wouldn't outright SOLVE these problems, it would just be a slight deterrent and a good source of feedback to brand-new players. It would only have significant impact on two specific play "styles": players who ROUTINELY start a match and quit if they don't get the first kill, and players who legitimately "give up" but quit in lieu of surrendering in order to find a new match immediately.
I am quite fond of the idea to not having achievements complete until the match is over. The type of people that ragequit are quite often the same type of people who care WAY TOO MUCH about achievements. Since the first several levels are fairly easy to net, I could see this having some effect on new players. By the time they are on achievements that take much longer, I would hope they have matured past ragequitting. I, honestly, wasn't aware that this was a core COD system.
I think that hot swapping would be a bad idea, it would definitely throw the balance of the game off. If there is not an opportunity for a crew/opponent to check out the loadout of a ship before it is launched, a large element of the current strategy is outright removed. If a captain could repeatedly change his ship or loadout, it would basically turn into a guessing game of rock, paper, scissors with both the enemy team and captain's own crew. I think the little "workaround" for switching classes, as well as the fact that it is widely unknown, is about as far into changing anything other than equipment mid game as we should get.
And I would imagine the opposite on 'crappy' CP games. If I have to call the enemy to the CPs using regional, if it's gonna be that kind of game, I usually find it to be over in one swift uninterrupted cap. Perhaps a little over 5 minutes, but the only 1+ hour CP game I played was very well balanced, with one single point separating the teams when the dust finally settled. If the enemy is providing significant combat that prevents me from capping all points quickly, even if they aren't exactly getting any CPs themselves, I still consider that to be a good match.
Finally, I do agree that the "replacement" captain should be on a volunteer basis, not necessarily just whoever is 'highest' on the crew list. This would at least let the co-captains talk to whoever is TRYING to fly the ship, rather than the usual random gunner. I always feel bad for that gunner...
On a tangent, if a pilot captain leaves a human crew of two engineers and one gunner, which role does the AI take; 2nd gunner or 3rd engineer?