I'd agree re: Morrowind's topography; I think Bethesda did a much better job with Fallout 3.
Agreed about having active elements that make the play interesting, in general.
Personally, I'd like to see:
1. Areas full of wreckage and hidden bases / encounters (not "hidden" like the "Pirate Base" from early versions, I mean real surprises). Early gameplay should, imho, feature asteroid mining, among other things; this was tested out in Vacuum and emulated a little roughly in other mods, and it was fun, as a non-combat way to grind a little money.
2. Areas where combat is totally prohibitive unless you're basically at end-game content (kind of like starting serious trouble in Earth System in EV...).
3. Areas where the player can dynamically improve the conditions in a variety of ways, from taking Bounty missions to clean out the immediate area of Pirates and other scum, intervene to end wars / border disputes, fix up a System's economy / ecology through various tools (building Stations, delivering items that can contribute to a permanent fix to ecological crises, etc.).
4. Areas where there's constant war between major Factions, putting the player in the crosshairs of opportunistic admirals looking for a bribe or booty on the side.
5. I'd really like to see "unstable wormholes" be the excuse for why Pirates can miraculously enter / leave Systems so that there is a little more flavor to travel in / out that supports "why haven't we surrounded the Jump Points with guns" and honestly, I'd like to see Pirate stations, rather than being permanent objects in Systems, be more "pop-up" objects that dynamically appear, support Pirate activities, and usually get destroyed by the main Faction in the System. That would add a huge dynamic feel to the game and players could help / hurt the Pirates by either destroying or helping to defend / found new Pirate stations.
But the long-term play is where it becomes more and more important to get a clear focus, and I'm happy to hear that Outposts / player-owned stations are looking like they'll become a real thing, finally. This idea of having the player make a long-term commitment to areas, rather than simply be an opportunist making money / grinding levels as the sole goal is welcome indeed.
Beyond that... perhaps what players need is to eventually have a relationship with the Factions akin to what was done in Mount and Blade; the player can subvert / suborn Factions, simply treat them as trading partners, or ally with them to achieve goals.
Perhaps each Faction needs to have an ending goal that players are instrumental to achieving, so there's something to do and real choices to be made. I know that's out-of-scope for this update, which is pretty massive already but I'm trying to think ahead a bit here.
For example, Tri-Tachyon might want the player to collect archeo-tech so that it can create a new Gate Network and escape the Sector to play elsewhere. The Dominion probably wants to repair the Gates and attempt to re-connect with the Domain and find out what happened. The Luddites probably want Tri-Tachyon destroyed utterly and the Gates demolished, because they're inherently evil and they want to return to medieval economics as soon as nobody has working space warships armed with nukes (or maybe they're just a front for something really sinister, lol).
The point I'm making here is that these goals can be done, from a programming standpoint, as pretty simplistic set-pieces (these don't need to be elaborate things, if the rest of the systems are already reasonably dynamic- for example, maybe the player declines the Tri-Tach quest because they're in a vice-grip war between the Dominion and the Luddites and the player doesn't want to get involved), but they'd add a lot to the fabric of end-game. I know that a lot of the UI / toolset for building this sort of quest is already in place, so this might be the way to go.