I really think that the orientation to a little more RTS game-play is a very good decision.
The game at beginning feels small, you got your stone ovens and steam engines but in the mid game you got like 20 ovens and many many miles of conveyor belts and then you enhance the factory and run around just thinking in tracks and inserters and how you can place everything the most efficient way.
I really dig into this kind of mid game, so real that i mostly forget about my player character and i try to place something on the screen border and it don't works and after clicking and short-therm-raging i realize "oh wait i must move my camera thing placeholder to get there". So i mean some people like this kind of attachment to the Character, well i like it too and the argument to identify with this guy has really a point but i think the coolest way to develop the game-play is to go larger and bigger.
So the Throne/Control Room idea is a good step to bringing the late game to Factorio and the more "larger and bigger thing".
It brings the game-play to a whole new level that you have now the big over view of your factory and you can plan and design much easier and it gives me a very sublimely feeling that i started this facility with just some stone ovens and now a army of building bots just waits to do my bidding and build up a whole new production line for armor piercing bullets.
The army part seems a bit more difficult. You have to think "do we really want the standard RTS select and click movement?" I think Factorio should stay with the passive control term (logistic bots). So i can think of some methods how this could work efficient and cool.
Building the units should really only be possible in a defined facility. I think about something like a modern car factory(
http://www.youtube.com/watch?feature=pl ... 82XBQhJ2Gc ). It would be so cool to build robots or tanks on a conveyor belt and one inserter puts the part on and one special welding inserter welds it to the chassi.
After they assembled the unit it walks of the belt and its ready to fight.
So now to the unit handling sure it cant be like "oke unit ready next stop alien base" it would end in a flash game situation where you just put down the facility and it spawns x units in x time so they can zerg-rusch the next base. It would work like that but it would be like i said "like a flash game" not the way the direction i would bring my game in.
So we need a more complex mechanic. The idea with flags or patrolling posts is nice and sure it would be useful anyways but i think you started with the colored networks why stop now?
Every unit gets a colored wire build in (i implicate that you plan to add more than two colors) and over this colored code you control your army's.
I'm not quit sure what the best way to control them is yet, maybe like place markers in the color of the army you want to move/attack or just make it work with the standard RS mechanic "select and order".
Maybe a system with radars that you give orders out of special Radar posts that control one army. the army only receive orders within the radar radius but it can leave the radius and finish the order even without a signal. So you build the red control post and order your red army to attack the next alien base. How the "give orders GUI" works must be consider then to. I saw that you work with coordinates maybe use them. Yeah it wouldn't be so intuitive and easy as "select and order" but it had a unique touche. And also it would provide some handwork(with your character), you could build a leaser and when you point on the ground and shoot it gives you the coordinates that you than can type into the red control station. After that the red army would leave with move/attack/roam/defend/explore orders.
So i hope i could make my ideas here a little accessible and didn't wrote a total mess, i await your constructive responses.
(maybe i add a little more thoughts later on)