Nothing on the map should be without a use or a purpose. By not making use of that I feel like this game, and the ones before it, are lugging around dead weight for really no reason.
At least that's my opinion!
Let me explain: On the map you have an assortment of objects. Right now you mostly have planets, stars, and asteroids. Starbases are constructed later on. Right now you'll sometimes have planets spawn with absolutely nothing at all. No asteroids or planets. Othertimes they'll have only 'dead' or 'uninhabitable' worlds (what's the difference?).
I maintain the notion that you're wasting your resources with this. First of all, the colonization of uninhabitable worlds is quite possible--simply inconvenient and difficult and modifiers to productivity can reflect this. I'd like to see various sorts of uninhabitable worlds like you guys had in the past, but things outside of the previous Extreme classification. Are they simply too hot, too cold, covered in a strange flesh-eating bacteria, what's going on? You guys had this in the previous game (Extreme Colonization, something I'm sure we'll see outside of the Alpha) but the one thing I do not want to see are worlds that you can do nothing with--what about Planet Mining starbases for the things you can't otherwise think of, a technology that lets you setup planet-wide mining operations? Like a super asteroid belt.
The possiblities are endless and I think it's a shame to see, including the full build of the previous titles, worlds that are wholly without purpose. If I can think up a number of things you could do with otherwise dead worlds I'm certain you guys can too! By the looks of it you already have some thoughts on the matter since you list two kinds of unusable planets right now.
I may very well be the only one who minds, though! We'll see what people say.
One little thing to consider is this: It looks like you guys consider every three 'rings' of hexes around a star to be part of the system. Inner, Middle, and Outer. Do something with that, I think it could be cool. What if ships can get trapped in the Inner Rings of supermassive stars unless they have certain propulsion? Luring enemies into that might be kind of fun! It'd also be fun to see, as a purely aesthetic point, if worlds in the middle rings around medium sized stars (such as yellow and orange stars) be the ones most likely to be habitable, roughly mimicking the habitable zones around real stars. In the same vein you'd find cooler stars with habitable worlds in the first ring and hotter stars with habitable worlds in the outer ring.
Galactic Civilizations 2 was my kind of game hampered by dead weight and a UI that I just couldn't stand. Galactic Civlizations 3 already feels better at an intuitive level. You've got this great thing at your finger tips and I'd love to see you do a lot with it. Fill the game with character, not dead rocks you can't touch.
As an ending note I'd love to see Survey Ships do more than just trigger anomalies. The idea of doing studies on planets, exploring them more thoroughly to trigger other events, would be pretty cool. Such as stumbling on an ancient lab (research boost) or a stockpile of valuable materials (cash income) or even awakening an ancient, dead, but super powerful Minor Race that immediately goes genocidal on everyone's asses like miniature, bunny-shaped (and they must be bunny-shaped) Dread Lords.
The world is your oyster and with the experience of two titles behind you guys I think there's a lot you can do. Stardock has never ceased to impress me and Galactic Civilizations 3 should be your crowning jewel.