I think a MMO strategy game would have the best shot at being interesting and balanced if it was split into shards of a manageable number of people, if the shards were reset once in a while (e.g. at the victory of one faction), and if alliances were fixed for the duration of the life of the shard to prevent the degenerate largest-alliance "strategy".
I have to agree here. To manage, I'm planning on letting players compete in live battles for control of planets. some large number of players controlling regions of a planet. The idea is that when you control a region, you are establishing an atmospheric defense system, which will only allow ships through of your side. But it only defends a certain portion of the sky. hence the regions. Once all regions are under control of your side, enemy ships can no longer get through to the surface, and the planet becomes 'safe' This leaves it more manageable.
Next, other players, who have attained a strong enough skill level/status in the game to produce a colony defense, can only produce squads that await orders in open battle fields. The players controlling the regions of the unconquered planets would have power to identify missions to take in battle space around their planet. (certain amounts of credit for this) Like Defend this area for 5 minutes, or take out an approaching tank armada. AI would have to determine the threat level, and spend a certain amount of special credits to send in an appropriately matched force for the challenge. So already many squads enter the battle field from assorted players on different planets, for temporary amounts of time.
I'm also considering the idea that AI controlled systems will be recognized by the same side. and that players can take over a fully AI run region of a planet. that way a battle and strategy can keep playing. The AI's would also decide on how to spend mission credits to defend the region if the player isn't. like 1 new thing every minute, or something like that, and if you haven't picked any missions in 5 minutes, it will then spend all but 1 of the credits on assigning random missions to help the planet.
However, I am starting to get to much into specifics on my own side. I will again point out that none of this is in stone yet, and I am still open to entirely different ideas and approaches.