(Just created an account, as well. I found this podcast via spacegamejunkie.)
This is a really interesting topic. I completely agree with the problems of scaling empires - managing a few planets isn't too bad, but once you scale-up to 20 planets, it starts to get really tedious. To be fair, the civilization games had this problem, as well. I usually get to a place where I try to gauge how many planets/cities I really need to manage in order to win the game (e.g. I only need to build on 5-10 planets in order to secure victory in the game) and ignore giving orders to the rest. Some sort of governor system would be helpful - though that opens up the possibility that players will enjoy micromanaging a small number of planets, but don't like the transition to using governors (while also not enjoying micromanaging a larger number of planets).
I've been thinking about this topic for some time because I was hoping a while back to create a space-empire game. I really haven't been that happy with any of the games that have come out since MOO2 (which was great for it's time, but it's a bit dated at this point). I agree that developers have been doing minor enhancements to the formula (or worse, they don't have the budget to actually carry-out their ambitious plans). I kept waiting for somebody to hit on the right formula to really push the genre forward within the past decade, but, to my surprise, that hasn't really happened.
The point about your population being just "workers" was spot-on. I was actually going to say "robots" - they produce things for your empire, but seem to have no needs or desires other than food.
BTW, I'm the developer behind "Empires of Steel", which came out back in 2009, but wasn't a financial success - which killed my ambitions for a space-empire game. I suppose there's Kickstarter, but I'm an unknown, so I don't have much faith that I could attract much attention.
One other thing I was going to say was that terrain and boundaries are different in terrestrial games like civilization. There's really no boundaries in space - your enemies can travel from any star to any star. This makes it difficult to do things with borders, like you can with earth-bound strategy games. You can setup choke-points. And if someone wants to attack a city in the middle of your empire, they have to travel through the rest of your territory. In space that becomes a lot harder, unless you can intercept fleets. But even then, there isn't any such thing as choke-points or terrain advantages.
As far as a 3d map, I'm not surprised so few games use that system. It's hard to visualize and wrap your mind around a 3d-map. It also makes the borders problem even worse because everything is closer together in a 3d world.
