I'm basically aiming at Remember Tomorrow. Aurora does a pretty good job of recreating the general principles of that game, but is far, far too convoluted for any average player to effectively get into.
So far, the general idea is an amalgamation of Remember Tomorrow's design and research, Sword of the Stars's race variety, and Imperium Galactica 2's colony construction and management. I have no idea how to make an AI, but since I'm hardly going to be able to get far enough with the game, I'm not too worried about it.
The science system is a "floating point tree" - the items all have fairly specific prerequisites in regards to other items on the tree (so no production-ready battlecruisers until you can build smaller ships), but it is impossible to specifically research any given item. Instead, you distribute all of your scientific power between General and Applied areas of science, and within those you select specific directions you want your scientists to take. Generic areas are Physics, Mathematics, Chemistry, Biology, Psychology, and whatever else that comes up. Applied areas are specific branches focusing on a definite goal - Optics, Superconduction, Antimatter, that sort of thing. Each item on the list has a pair of prerequisite sets. Upon reaching prerequisites in the first set, you become aware that the item is achievable - it shows up in your research lists, and you can see what areas you need to progress in to reach the second set of prerequisites, at which point the item becomes production-ready (or gets implemented, or anything else depending on the item). But, since having very definite progress prerequisites would prove boring after a couple of playthroughs, there's a degree of randomness in there, and there's more than one set of prerequisites for either showing the item or making it available. Sometimes, it'll be possible for an item to become available when it wasn't even visible at first, which could result from suddenly hitting a second prerequisite set without triggering any of the first.
The ship and unit design was initially going to be less complex, but seeing Aurora I thought it'd be neat to have this kind of detail as well. You're still going to rather directly fill out the "hull" of whatever you're designing with various components, but it's not going to be slot or weight-based. Additionally, you'll be able to design custom weapons using whatever tech you have available - in addition to the weapons your scientists come up with by themselves. The intent is being able to, if it's so desired, to have launchers for ramming torpedoes that carry powered-armor boarding crews, even if it's too ridiculous for the game to have it included initially. Power systems and life support will be vital, and their placement will have effect in combat.
The combat itself is the difficult part. Initially, I thought to have a realtime brawl using simple graphics and a physics engine, but now I doubt it'll be all that good. Especially if there's going to be any multiplayer. So, I guess Aurora's battle design is good enough, but there will be graphic representation. Each ship is going to be a volumetric model (even if blocky and displayed in ASCII if it comes to it), and each projectile impact will be calculated. So no hitting the ship's engines while randomly shunting torpedoes at its bow. Unless your torpedoes are strong enough to punch through, of course. Component position will matter here. If you have fuel tanks close to the hull, a lucky hit may quickly take out the entire ship. Same goes for big blocks of adjacent generators which may be explosive, tiny nigh-unhittable vents that lead straight into your core reactor, and having very thin connections between ship sections. I'm not sure how much load that'll put on the processor, but I hope battles aren't going to be fought by thousands of ships. Initially, at least.
The command structure is something else I thought about. Ideally (and optionally), you're not going to personally have to watch battles unfold, instead you'll receive reports and issue orders from afar. If you do happen to stand on the bridge of your command flagship heading into the heat of battle, you will have that degree of control, but will instead only receive brief reports of your empire's workings. "Overly ambitious" plans include simulating you as a person. As in, what you see is what your character sees. If you're in your office, you will monitor the empire, but you won't see much if you just stay there. Instead of choosing different "wait times", you can also perform different actions. Training combat skills, running simulated battles, participating in public events, etc.
That's all I can type down now, gotta go. These are all just ideas, and I'm not too experienced a gamemaker, but stuff like this is usually fun, so I see no reason not to try.