Limiting player growth by harsh in game rules will dampen the end-game experience. Whats the point of striving for victory if you have nothing to gain except limitations? There are few games out there that I've seen that can really boast a persistant world, in combination with an RTS, and MMORPG. The main reason is usually the devs wish to create an environment persistant with a linear story. The main draw back of which is obviously ''How can we integrate an RTS into a story''. So they dream up ideas to limit player interaction to skirmishs, agreed PvP, or non-effectual (but fun) large scale encounters. I can't say I've read deeply, thus far, into your game, but on the surface it appears you're heading in that direction, so I chose to reply to this article in particular.
In my opinion the best solution to the problem of player limitation is either to constantly expand your universe, which can be done through quest packs etc.. which you could possibly charge for, or better just reduce the concept to a round based game, which in and of itself would introduce some other fun aspects into the works.
Imagine setting various variables as far as planet types, nebula, asteroid fields, distrobution of resources, NPC factions, quest hubs, black holes, white dwarves, what have you.. that you might like to see in a universe, setting a list of these variables and building a randomising program as opossed to a static universe would free you to make a complex and varried universe, yet completely different each round.
The over arching story can be the same, certain factions may continue, but it gives the players a chance to sieze land, build empires, and actually play the RTS factor of the game without being limited to instancing.
As far as questing, trading etc.. you could even integrate a randomisation of quests.. say only 30% of total quests created will appear in any universe generation, and factions may change in strength, wealth, or even personality.
Just some thoughts as it seems you guys are right at the start up phase of operations, and I do hope I didn't offend anyone.
-AlfonzFred-