How about this:

You join up with a small group of 8 or 9 other people, and you all joint-control an empire.

It pulls out the #1 selling point of massively multiplayer: society

This would bring a whole new level to strategy. For example: When you wish to attack, you could plan for everyone to show up and help control the battle.

I suppose there would have to be some limit on the number of people joining an empire - mabye 10? Or perhaps the max number would grow as the empire takes new planets.

I''m not sure if this is what you were asking or not, but I think the most simple way to do this is obviously to have offline bases run by AI with customizable scripts. If this is an in-depth RTS, I''m assuming you''d have a lot of micromanagement when in charge of a base, so leave out all but the most necessary of functions when a player goes offline in order to save processing power. Maybe just allow the player to leave his resource gatherers running, something along those lines.

As for defense of a base, I believe this is a much easier situation. Leave it up to the player to defend their own base, give them plenty of options as far as base fortifications and defense units go. Emphasizing or even requiring player alliances would be an enormous boost, allevieting the offline defense problem as well as fostering a more social environment.

I think the big problem with a persistent world RTS is the tax it will put on the players'' processing. With the world constantly changing and growing, it would be hard to keep initial load times at an acceptable length. Like someone said, it would be easiest to make the world very large and spread out, and have the player''s client update the world as they move throughout it. Still, this would require some major server power.