Well I arrived at the discussion late. I think the ship scramble and crew/ship swap would be nice features to have. I think a lot of the issues raised come from a misunderstanding of how it's intended to work.
http://gunsoficarus.com/community/blog/november-at-muse/From what I've read, I can't tell if it's planned to be an option at match creation, or mandatory
We actually thought through the logic and logistics of where best and how best to implement scramble, and ended up preferring scramble at match creation over voting for a few different reasons.
This post makes me think it's an option at match creation, although the initial blog reads that it would be mandatory in public matches. Personally I feel an option at match creation would be best.
But how it would work is a whole ship swap, taking 1 ship (maybe?) from each blue and red team and having them change places. So instead of team A and B vs C and D, it could end up being team A and C vs B and D.
This means the crew composition on the ship is still the same (so you're still playing with your friends if you're an organized team), and you just have to worry about coordinating with your ally captain(s).
The scramble would take effect after X amount of consecutive wins based on the team (red or blue). In their example, this number is set at 5.
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Regardless of how it works, I don't think it would do much against "stacked" teams. Teams that are stacked and wish to remain so have pretty easy workarounds, such as forfeiting/losing on purpose right before the win streak reaches the threshold. Thus the count is reset and they can keep it up longer. They might not want to lose and just choose to leave the match and create a new lobby. This isn't too bad, as the thought that this will create piles of half filled matches doesn't take into account a player's desire to actually play a match. If the lobby doesn't fill up, they tend to leave it and search for a different lobby. It's an issue that tends to resolve itself.
Then of course the ship/crew swap just might be 'abused', with the previously stacked team ships refusing to start the match until the other captain lets them swap back. In the same manner that players will refuse to start a match until their crew members bring exactly what the captain wants them to bring, and on occasion refusing to start a match until that crew member changes places with one of their friends who they want on their ship.
Then there's the negative side of the scramble. What if teams aren't stacked, but one team still ends up winning 5 times in a row? Maybe it's two pub teams or even two organized teams going head to head. Each deathmatch ending 5-4 or 5-3, one team just barely coming out ahead each time. The scramble would still go into effect. Of course they'd still have the option of crew/ship swapping, but it's just something consider.
Overall it's a nice option allowing for variety and better competition at the unorganized team level, but has a difficult time reducing 'stacked' team situations (in the events where they wish to remain stacked). For organized team matches, it should be difficult for them to reach the win streak necessary for the scramble, and even if they do it's more likely they'd just swap places back; making it not affect them at all.