This talk about stacked lobbies is old, but I am going to play arm chair designer and come up with a completely different lobby/match making system that hopefully reduces game wait times, spreads the pain of fighting stacked ships, rewards high level play, and dynamically resizes to run 3v3 and 4v4 games depending on player population.
The core idea behind this system is there is no rematch option and the performance of a ship as a whole is the determining factor for its placement in match making. Instead of joining a match lobby players will join a 4 person ship lobby. The ship lobby will have a rank assigned to it based on its wins/losses. This rank will determine which ships it is matched against and how much faction prestige and coin the players on that ship will receive per game.
New players can join the ship lobby and old players can leave and the ship will keep its rank, however if all players leave the ship it will be disbanded and all ships below its rank will rise 1 rank value. Players can create a new ship lobby at any time but that lobby will start at the lowest rank until they work their way up.
While in the ship lobby the player in the captain slot will have the ability to change the ship's load out, make equipment load out requests of the crew, set ship lobby settings, and filter for the type of game they want to join. The captain also can hit the Ready button to put the ship into the match making Queue. The Queue will dump 4 to 8 ships into a match lobby with an unstoppable 30 second timer until match start. This will give captains a short window to change ships to counter enemy builds or better conform to the map. However by readying in the ship lobby they have signaled that they and their crew are combat ready.
If all players on a ship leave in the 30 second match lobby or during a game play a new ship waiting in the queue can be pulled in to replace the missing ship. That ship will be given the same 30 second timer to asses the lobby before joining it. Also the players abandoning their ship mid game will loose their ship lobby's rank.
The previously mentioned lobby settings dictate how people can join the ship. They can set the ship lobby to accept a player any time, only while the ship lobby is not in game, or lock the ship completely. While a ship is locked the only way a new player can join it is through an invite by the some one already on the ship. Players that get DC'ed can still rejoin within a time period (like they do today). The lobby settings also allow the captain to set a short advertising blurb about the ship lobby like: Clan recruiting, Russian speakers only, PvE for the Yeshan Empire, ect.
Players looking to join a game can create their own Ship lobby or see a list of existing ones. Each ship lobby in the list will show its rank, population, friends of the player (if any), Current game state, lock state, and captain's advertisement text. Clicking on a locked non started game will send a private message to the captain requesting to join the ship. Clicking on an unlocked game will put the player in the ship lobby.
At the end of the match each crew will told if their ship's rank went up or down and how much prestige/gold the player got based on the outcome of the match. Since they won't be returning to the same match lobby players can jump out of the post game screen at any time to return to the ship lobby.
Since people will spend less time in match lobbies there should be a series of "taverns" for players to socialize while they look for a ship or wait for their ship to deploy. Taverns should be on a separate voice channel from ship lobby so players can organize their crew or recruit from taverns at the same time.
If a troll joins a ship the captain and crew can leave the ship and form a new one to exclude the troll. The troll will inherit the ship's rank while the original crew would start at the bottom, but the troll will be matched against more experienced crews due to their higher rank and probably get crushed until they rage quit.
An option for a custom lobby should still exist separate from the ship lobby for clan matches and tournament play, but most players would find their game through the ship lobby match maker.
TLDR;
Remove the Match Lobby and do match making on a 4 person Ship Lobby. Give captains more control over who is on their ship at the ship lobby level. Move the social aspect of the game to chat rooms called taverns.