Before I start with my suggested concept for a Sins MMO, I will give some background information on a web browser game called Travian. It is upon that game that I drew my inspiration and realized that SoaSE could do it so much better.
The Concept:
Like Travian, a massive game play area would be established. As more players join the game more stars would be generated leading to a expansive procedural universe.

Each time a new star is created it would receive an (x,y) coordinate based off of its position. This will be important for calculating distances as well as travel times between star systems for player interactions.

Just like the current RTS, if you have vision of one of these star systems you can zoom in and then the play is identical to the SoaSE RTS.

The major contribution from Travian is the game pace. And this in many ways is the reason why Travian has been successful and other MMORTS fail. The pace of a standard RTS game ranges from 15min to a few hours. Far too short for a MMO thus MMORTS get boring quickly. And so, my suggestion is build times of ships, structures, titans have more of a Travian pace. And so would travel times between star systems/planets. It also allows for more deliberation and strategy on each move as sending a fleet to a distant star means you can't get them back for a long time in case of invasion.

Build times would range from a few minutes for a frigate to a few days to construct a titan. And like wise resources would collected even if you were offline as in Travian.

Game play:
Game play would consist of a player creating an account and at that point an unoccupied star system would be the spawning point. If none exist the game would generate a new grid of star systems. A player would start with no planets or structures. Just a single capital ship that can establish colonies giving the player two options. Establish their planet in that star system or phase jump to another star's coordinates. This would allow friends to play together or loners to go their own way. While other players can settle the planets in your system if you haven't already, no two players spawn in the same system. Early game for a player should consist of taking planets and dealing with pirates.
Midnight attacks?
One of the biggest issues with MMORTS are the midnight raids while you are sleeping. Travian deals with this in three ways and would work for this concept as well.
1. Hours to days travel time to distant stars.
2. Notification of inbound enemy forces giving defending player time to prepare.
3. Allowing allies from different time zones the ability to come to your aid through the use of alliances.
I thank you for your time.