Ya, I see several difficulties too. What would the UI look like? Would it be a seamless integration of planet development and empire or a double turn of Part A and Part B? Is it possible to make this a single player game?
Looking at the initial premise, I think it is one solution to the problem of too much abstraction in the environmental elements ofthe space setting. Mechanically, having players directly manipulate the map, and tying in power growth dependent upon the planetary side freshens the dryness of it. However, how to get player buy-in to the division?
Would it be better to have one's planet on the same map? This could allow a single player game. However, it changes how the tech tree functions. I originally see the individual planets as the source of tech advances, not the empire side. Empire is about control of the theatre, and offense and defense. The planets would be the sources of supplies, ship building, technology, and culture. So, putting splitting those elements into a separate game that intrinsically effects the wargame side really is intriguing, eh? There could be diplomacy going on in both Empire and Planet, but of different kinds...
I think the idea would work best as an MMO only.
I'm not sure if it would be best to originate one's empire from one's Homeworld, or to separate them but on the same map, or to exclude the planet game and the empire game. Ultimately it might work best to keep it simple and locate both aspects of the game on the same map.
Perhaps there would be a technical solution to try both types of games, have one's empire come from one's planet, or, have one's empire come from someone else's planet.
BTW, I've been listening to your podcast since last fall. I think you guys are brilliant.