I was about to make a post on this very subject. I recently joined the game after winning it on a Twitch giveaway and I've been quite impressed. But far and away the most-disappointing and frustrating aspect of this game has been getting into matches. Almost invariably, you find yourself on a random ship of unknown configuration with no plan. While it seems like it'd be a great game to play with friends, my friends aren't interested in paying for a game with such a low population and uncertain future. (Though if there's another great Steam deal on the 4-pack like I just missed, I'd buy it for my friends.)
I too was going to propose a multi-stage matchmaking system that promotes, but doesn't require, some semblance of organization because, frankly, being on an organized team against a disorganized mob is just as uninteresting as being in the disorganized mob. I don't think finding a "good" crew through chat gets this game where it needs to be if said good crews roflstomp the competition to the point everyone gets frustrated. The game's design should promote the learning of good habits from the get-go.
I think players should first be matched into crews through a set of preferences relevant to the individual (e.g., server location). In the crew matching room, players choose their roles, can see the selected ship and its loadout, or even enter practice mode. When all crew members have readied up, the commander then finds a match for the ship. One of the preferences for crew matching can be "fast action" vs "strategic" or somesuch. Players matched into a fast action crew are automatically marked ready after 30 seconds, so players wishing to just "wing it" in the way that seems pervasive currently may continue to do so.
In addition to promoting good play habits, I think such a system would help players form new friendships in a way the current system doesn't do very well.