Good ideas Osidlus.

It's a tough balance to get right. The hard part it seems is giving the weak players enough of a chance to make a comeback, without having the game go on forever in an endless cycle of power shifts or be too random.
I got a couple of metagame related game design questions. These involve not my initial (limited in scope) game but the down-the-road Admiral interface version.
protectorates : problem #1 : social/guild (metagame)This goes back to the first reply to the thread. I go back and forth on this one, it seems to have huge potential but I've ran into some serious issues too. The problems relate to the metagame. In casual play I think it might be fine, but imagine this scenario:
You have 5 highly-skilled Guild teams (I've made no provision for Guilds at all at this time, so assume these are voluntary player-formed organizations/teams). Each of these 5 Guilds is matched in a pre-made game (or Ranked team game if that is supported at one point). So you have have 5 teams, each team with 50 players of the same guild.
Now, the game is going on, and the weakest Guild/team which is on the verge of extinction agrees to become a Protectorate of one of the remaining teams. Basically, the fundamental problem here is social. You have an enemy Guild that is now playing under another Guild. Would they ask for Ventrilo server info? Would they be privvy to trade secrets such as they find out that this Guild always does a feint in their wormhole event or what have you?
Perhaps these questions could be addressed by keeping the Protectorate players segregated. Eg, while they are now aligned with a stronger Guild/team (for purposes of 1 single game), they still retain their own Admiral who gets orders from the primary team (the one they merged into)'s Admiral. In other words, the more powerful team could still have mechanisms for giving orders to its Protectorate, but there is a barrier in the sense the Protectorate doesn't gain 100% of the winning team's data (including Ventrilo most likely but that is controlled individually by the Guilds).
Also, I realize these social problems would probably not happen in the vast majority of games, which are pickup (random player) games. It is only Guild games and pre-made games (assuming these are supported) that these social issues are even a concern. In random games it is perfectly fine for 100% coordination/assimilation of the protectorate into the more powerful team because these players are independent anyways so there are no trade secret tactics.
protectorates : problem #2 : newly assigned player (metagame)The second problem I consider minor, but still something on my mind a bit. It is that when one team is a Protectorate, in pickup games they will have turnover. In other words, players will leave for all the obvious reasons (parents came into their room and asked them to do dishes, they are late to class, lost internet connection, got a phone call, got bored). However, when a player leaves, a new player from the queue will replace them. The new player will probably be unhappy to be assigned as a Protectorate since it means they are guaranteed partial victory at best, without the possibility of full victory.
I don't see this as necessary a terrible thing, as I'm pretty heavily influenced by Netrek's player rotation which was effective. Yes, sometimes you would join on the winning team. Sometimes you join on a losing team. The best was you join a game that is in balance or was just about to start. But even so, it wasn't really a big deal if you joined a losing team. You would just lose, or possibly have a long but rewarding comeback, and still have fun. Then you would play another game or two, this time from the beginning (or 5 if you were an addict like me

).
So this issue isn't specific to having protectorates, this is an issue the game already will have regardless. But having protectorates exaberates the problem since there is no way to do a full comeback as a protectorate. Even if your combined team wins, you get only partial victory since you were randomly assigned as a protectorate player.
Admiral interface : supply / demand (metagame)The next issue I'd mention is not related to protectorates, but is yet another metagame issue related to the Admiral interface. For the full version game, I was thinking of having 50 players to each team, eg 1 Admiral and 49 starship pilot players. With 5 teams that is 250 total players. I like that scale in terms of it would seem to give an epic feel, but not be so many players you are completely lost as just a number (though perhaps borders on that).
The big problem I see is one of supply and demand. There are going to be more than 1 in 50 players who want to be the Admiral. This is partially addressed by charging money for the right to queue as an Admiral. The game is fremium model after all, and what cooler upgrade is there than the Admiral interface? Even so, my worry is many players would chose to purchase the Admiral upgrade and still not be able to be assigned that position nearly as often as they would like, due to the odds.
One idea is reducing the number of players per team to 20, down from 50. That would substantially improve the ease of Admirals to play more frequently (getting into the game as a starship pilot will be nearly instant). But, with 20 players that is a less epic feel than 50 players per team. I want there to be enough players that you can spread out among the various sectors, often in groups of 2-5, so I don't know.
For now I'm tempted to leave the design at 50 players per team for the full (Admiral interface) version, and some of the ratios in terms of queues are probably too hard to predict without beta testers etc, but it is something to think about.
I don't need to answer these issues now as that is all for the full version which is way down the road. Still it is good to get some of it preliminarily mapped out so if anyone has thoughts please chime in

I'm on vacation in a few days until Oct 7 so won't be responding for a while, apologies in advance for delayed response.