Yes, we will need sub-factions from the main races; we can make these up ourselves. We pick an arbitrary number, say 3 sub-factions per race, and then people who are interested in those races may head up the factions, name them, create basic lore, etc. This is for the RP buffs amongst us.
Technically, the sub-factions are already created for us: there are 10 different AI names for each race in the game that are the sub-factions. They lack lore and background, and personality, but they are there.
The "Galaxy Map" in my mind is a vast series of "star clusters". Star clusters are, obviously, made up of stars, which is convenient since this is the basic element of any Sins map; each map must have at least one. You may remember star clusters from Battletech, though they mean different things. Hopefully you can see where this is going (different clusters, different number of stars, etc.)
I wouldn't use a star cluster. Multiple stars add a huge amount of time to finish a game, and the fewer the players the worse. If there's a "star cluster" with 3 stars but only 2 players from each side are committed to play.. well, you get the idea 
I think it should stick to solar systems exclusively. Even 5v5 can fit comfortably on a big enough single-star map. The added bonus is we could have characteristics per-star. A Sol-type star is much more ideal for supporting life, so its map would have more terran planets, for example. Outside the game, this would also work well with the logistics: different solar systems contain different total populations, affecting income/production.
This we can make as complicated or as simple as we want. A couple ideas:
- Each system has a "production value" per turn. The total sum of the production values dictates how much you are able to spend on your forces that turn, among all of your battles. For example, let's say a faction owns 40 production per turn, they want to attack one other system and have to defend 2 of their own from attacks. So they have 3 battles and 40 points to spread out among them. They can go and do 13 points per battle, or do 30 on the attack and 5 on each defense.
In-game, the points would translate to the fleet point level they are allowed to reach, going in something like 10 points per level, not counting the first. So committing 40 points to a battle would allow them to research fleet upgrades 4 times. On defense, we can assume "militia" defense forces that come into play if the defender commits x less than the attacker. For example, if the attacker commits 40, and the defender only commits 10, the militias can bump him up to 20/30.
Obviously, when a battle is declared the faction leader has to specify how much he is deploying, and this would be visible to the faction challenged.
- The other idea is to do income-based and have it influence attainable tech level. No point system per battle, just however big your faction holdings are. So say making 2 million credits/turn would allow you to get to tech 2, 3 million tech 3, etc. The connection here is a bit more loose than points to fleet supplies, but it's less to keep track of. Each system would also be capable of producing x credits/turn so some systems would obviously be more lucrative to hold, and would also be prime targets for attacks. The downside is once a faction starts losing, it would be very hard to recover. It would need to be made so a faction is allowed a few concurrent losses before dropping a tech level, but once it happens it can be a huge difference.
- Of course, those two can also be combined
The hardest part of all of this in my opinion is hashing out the different "power-ups" and other such abilities that controlling particular clusters allows a faction (starting resources, ships, ad infinitum). Basically, we've got an open slate for this and it's entirely up to us to create a balanced yet fun universe to play in. I'm sure the folks who created Sins know all about the difficulties of that.
I really wouldn't make bonuses/power-ups specific to systems, though. The starting resources model wouldn't work well because starting resources are set by map so the maps would have to be re-done for each fight according to who's fighting on it and it's a nightmare. It also doesn't make sense that controlling one system would allow you to build some ship that you couldn't otherwise.
I would vote to just have various economic characteristics (they could even have trade values per turn) and base what ships and how many players can deploy on the total faction income from their owned systems.
In essense, this is what SCL did. It was like a pseudo-grandRTS. The "campaign map" was done on the net outside the game, and the game was for the tactical battles. The easiest comparison here would be the Total War games. Just imagine all the movement, politics, economy, etc done outside the game and just the battles take place in-game.
