Should the player be a human or a Cocytian?
I think that it would be rather difficult to identify with the Cocytian because they are alien, and, as is well documented in the novel especially, their "thinking patterns" would differ from humans'. In order to maintain a realistic storyline, I don't think the player could or should be a Cocytian. That's not to say that a living Cocytian couldn't be part of the player's group, just not the player himself. In fact, it would be both interesting and useful to have an alien in any group
As far as location goes, I agree that returning to the same place would make no sense, and that going somewhere else is also a bad idea. Certainly, though, it would be interesting to see what they'd done with the place since we last saw it.
These days, I'd like to see the ability to travel all over Cocytus. It'd definately take a long time to repopulate an entire planet, and therefore there would be many places reflecting the desolation of the space port. But, you'd lose the whole mysterious element if you knew where you were.
Now that I've thought about it, I'm not sure that you could really fully replicate the nature of the first game. I remember when I first played it, and first got to Cocytus, I had absolutely no idea what was going on. Almost everything that happened was a surprise. I believe it would be hard for seasoned Diggers (now there's a word) like us to recapture that feeling. Hopefully I'm wrong.