Some games you are gonna end up with 3 powder monkeys, but eh, can't win em all.
Commanders could be given "at most" crew class limit buttons for their ship for each class, with pilot defaulting to 0 (commander doesn't count against this), gunner defaulting to 1, and engineer defaulting to 3. Clicking the class icon would decrement the limit (so clicking on gunner once would indicate that zero gunners are desired), and roll around back to three when clicked on zero.
Monkeyism can be dealt with in a number of ways: the most straightforward seems to be "max level minimums", which cannot be lower than the current class level. For example, if I am a level 8 pilot, level 3 gunner, and level 4 engi, my max level is 8. A level 5 pilot (regardless of their other class levels) could set the level limit to no lower than, say, 2 less than their current level -- since my max level is greater than 3, I could fill their crew slot. If they were level 10, they could set the limit to 8, and I could still fill their slot, but someone with 3,3,3 class levels could not.
What would stop people from simply "down-thumbing" for lack of skill, or the fact they just don't like them? Then you get all these false representations of players for reasons other than being a straight troll.
Level 3 always seemed like a "graduating to competence" level to me, where game mechanics knowledge is well enough rounded that the player
should know what they're doing. If they're max level is less than 3, they should be protected from thumbs down. Otherwise, thumbs downs should not be allowed unless at least 3 players give it (or in a 2v2 match, at least 2 players give the thumbs down). Regardless of the numbers of thumbs down, at most one should be recorded per match.
The fear is that people will start kicking new crewmembers instead of trying to teach them the basics.
There are already achievements that reward playing with low level crews.
And since non-English speakers tend to be silent, it's hard to know that they're not intentionally being douchebags and really just don't know that taking the front gun and not shooting is a bad thing.
There's also a problem with people without mics (who do speak your language) needing to type it in, taking their hands off of repairs, gunning, etc. This could be solved with one or more menus of common communiques (such as you see in Team Fortress, et al), that translate into the receiving user's language. User's languages could also be indicated in game, though you'd want to avoid using 'language flags', since these can be offensive to users who speak a language but don't live in the country indicated by flag.