Whoa, that's a pretty epic post there SubArtic, cheers for the suggestions!
Myself and CWolf have already talked about a lot of the concepts you have raised here, some we've already planned, some extending onto what we already have and others we haven't but may be willing to implemented, etc.
I will say one thing though, the RPG/explorable world, while being a great idea, kind of goes against the scope we've set out for this game, I'm afraid. What we are planning is infact something that does resemble Uplink to some extent (with a lot more things to do, making good use of the multiplayer aspect).
That being said, there are some truly great ideas here
we'll have to work out what we want to incorporate. I don't think any of them would get into the alpha though
Thanks again!