big setback for the fsrts mod was lack of dynamic waypoints, so move commands didnt work reliably. we never got to the point of figuring out resource gathering or base creations (of course we never planned to do this, it was always you get x assets to finish mission y).
I just had an ingenious idea! It's a silly workaround, and if dynamic waypoints or "move to position" orders ever get proper support it ought to be redone that way, but...
You could achieve something like a move order by ordering a ship to dock with a ship... make the target ship invisible, no-collide, on a team that nobody attacks, etc., and once the two ships get sufficiently close, cancel the dock order and remove the ghost ship.
Of course, there were a few other issues in the way of making a proper RTS... for example, the Escape key behaves; in an RTS, you want to be able to cancel actions with that key, but in FS2 it brings up the end-game menu.