Ultimately I think matchmaking is a good idea, for a number of reasons. The big disadvantage is that we do lose some choice in the matter. However, part of the matchmaking goal is to put you into fair matches, something most players try to look for anyways. You might lose the ability to randomly create some 'for fun' matches like all mine battles and flamethrower wars, but there's a custom match for that.
The biggest issues I come across in the match list system are long wait times to start a match, and imbalanced matches. The scramble option helps relieve some of the imbalance, because it keeps shifting around.
Wait times prior to a match is caused by a number of factors. First you need all captains slots full, then you need all captains to ready. Captains only ready when they're ready, and they often wait for everyone to be ready because we're full of happy go lucky friendly people that don't like force starting a match.
For a single captain to be ready, they have to be prepared for the match. This can range from a player just being happy they're in a captain slot, to a captain making sure his crew and his ally ship meet his expectations of loadouts and experience. How long this takes depends on the crew's knowledge and experience.
Most captains also want to have a full crew.
Match imbalance happens for a number of reasons, and most of them aren't intentional. Players want to be on the 'winning' team, they'll flock to the higher ranks, or they'll want to play with their friends/clans. Newer players tend to leave more often, letting more experienced players stick around and start to group more.
You toss in matchmaking, and those issues start to go away. Matches get automatically filled with players around the same experience/skill. Higher ranking captains tend to have higher standards, and these are more rapidly met by higher ranking players who know to do what their captain expects. Lower ranking players don't have that many expectations, and they'll often get a crew who's happy to do whatever.
Matches will also be fair more often. The higher ranking players will be congregated together, but they'll also be put against other high ranking players. This leads to much more interesting matches. This also allows the newer players a less steep learning curve. As they get better, they'll be put against players that are better, and slowly learn the game rather than being tossed into the deep end of the pool under the system we have now.
I've also been informed that this reduces the load on the server by creating the optimal number of matches instead of having 50 matches waiting to fill up when they each have 60% of their slots full. (where 30 matches would be the optimal number).
It might also improve the appearance of different maps (such as 3v3 and 4v4 maps). In my ideal matchmaking system, you'd just put in whether you prefer a capture point match or death match, instead of choosing a specific match you want. The increased variety would appeal to a lot of players instead of doing dunes over and over because someone needs the achievement.
Obviously it's not going to work 100% of the time. There's going to be times when teams aren't balanced, or it takes a long time to find a match. That's just life. But it certainly would improve upon what we have now (in terms of wait time and balance).
You can still group with your friends, and start your custom matches by inviting players; so I don't really see too many downsides to the system. This has been thought about a lot, even up to ways to keep the socializing factor still around. Overall I think it'll be a solid system that improves player retention and general enjoyment of the game.