Whoa, that's a lot of questions - let's dive right in!
Is the whole "inevitable decline" theme inspired by Foundation?
Never occurred to me (been a long time since I've read those books), so perhaps only on a subconscious level
I just happen to subscribe to the "losing is fun" mantra, and don't think enough games out there do that.
In the later game, will the player be able to effect the universe at large? For example, at a certain level of technology, you could start building mining outposts on asteroids, later on maybe hydrogen catchers orbiting stars, artificial planets, etc?
You wouldn't have to wait that long - mining outposts etc will be something you can set up shortly after you start playing. As far as affecting the universe, the philosophy is that more power means less control - so you can have an impact early on if you know just where to strike. For example, intercepting a lightly-escorted refueling fleet might force a far larger task force to retreat - so you can shape the conflict between two factions without having to outright defeat their fleets.
Will there be gravity?
Yes, right now it plays a role in combat. It will also affect travel speeds - nearby stars, planets, etc mean you go slower - so going through deeper space is a shortcut, but has its own dangers. You can hug the coast, so to speak, by staying near star systems - or you can go fast and take your chances in deep space.
What's the timescale for the game? Will it occur over years? centuries? will we be able to change the speed time passes at?
Time is kept in sector cycles, which are roughly analogous to years, but fuzzy enough so you can imagine them to mean whatever is appropriate for the situation at hand. You do have a character, though - you're not an invisible, omniscient force controlling an empire or a people - so the overall time of the game isn't measured in centuries.
Will players eventually be able to create dynasties or empires of their own?
You'll be able to build outposts on multiple planets, organize fleets, have relationships with other factions. Core worlds (worlds with a large population) are a limited resource, though, so the only real way to get them is taking over existing ones.
What about genetic modification?
Nothing planned.
How is the research system going to act? Will it be semi-random, like the inventions in V2? What's the scale of it: Is it just going to be small leaps forward, or is it going to stretch on into super advanced stuff like gravity manipulation, time travel, etc?
Most "research" actually involves uncovering lost blueprints from ruins of now-decivilized worlds. The blueprints are used at auto-factories (which can't be built anymore - the knowledge is lost) to create whatever the blueprint outlines. Check out
this post for more info.
Will players be able to design facilities to build on planets?
Will mining be abstracted, or will it be more detailed, like mining facilities removing ore from the planet, with the efficiency dropping as you get deeper or further away from the mine?
You'll choose which buildings to place (extractors, refineries, storage silos, etc) and where (relative to resource nodes and such). So you're designing the outpost, but not individual buildings.
Will resources be abstracted down to the typical "food, metal, luxuries" type stuff, or will it be a full array of resources?
It'll be more involved than, for example, rts-style resources, but I don't want to have complexity for the sake of complexity, either.
Can ships be made out of different materials? And will they behave significantly differently if so? For example, could an iron based hull be affected by magnetism, or an extremely dense hull require stronger communication devices?
No.
Once a player gets powerful enough, will the game transition more into an rts? will we be able to take care of the particulars of running an interstellar empire?
Depends on which path you choose, though never quite an rts. You can build up more of your piloting and combat skills and precisely control a small but elite force, or you could have a larger set of holdings, several fleets, etc - at the cost of much control. You'd still control your main fleet and flagship, but of course they wouldn't be quite as good as if you focused entirely on them.
Will there be randomly generated worlds? or will it be reliant on pre designed maps?
A bit of both - some pre-designed key worlds/systems, and the rest randomized.
Will the universe physically change over the course of the game? Will stars grow and eventually die out/go supernova, will new systems be formed from nebulae, will planets gradually change in habitability or chemical composition as life flourishes on them?
Will the player be able to seed life on barren planets?
Will there be terraforming? and how in-depth will it be? Will it simply be a habitability factor that changes over time, or will you actually be able to change the atmosphere of a planet to suit certain purposes? For example, perhaps a farming world would benefit from higher CO2 levels in terms of productivity, but raising it too high would make it too hot for certain plants?
The time scale isn't right for this type of stuff.
Will the player be able to use weaponry to kill off life on planets?
Yes, and not just the player.
will resource shipments rely on freighters?
Will the economy respond to supply and demand? For example, say I bring 10000 tons of steel to a shipyard planet. Will they pay more than a farming world would? and would the price dip temporarily once I sold it?
Yes and yes.
will AI traders move resources from planet to planet? And if they exist, are they trying to make a profit, or are they just a mechanism for AI's to transfer goods?
Both - if the economy is based on supply and demand, then moving goods around to satfisfy it will also be profitable. Some traders are more independent, though, and will do longer and more profitable runs, while traders owned by a faction will do what the faction needs.
Will individuals have dispositions towards certain factions? For example, say an administrator of a mining outpost has a bad history with a faction that I'm officially neutral with. will he decide to shoot if they come too close when another person wouldn't have?
Hmm, interesting idea. Can't say just now - depends on the details of the relations system.
I hope this gives you a good idea of the game's direction - but please bear in mind that much of the higher-level gameplay isn't implemented yet, so the answers reflect the current design, which may very well change when it's battered by implementation and playtesting.