I still believe the setting is mature, BTL's, open prositution never mind the bad language etc. I would have thought that content restrictions would come as it is at its core a game, and so, despite not needing a physical copy would come under the rating systems. Of course I tend to work on my own concepts as full production titles, so I am not as as aware of the state of things as I probably should be in regards to this project.
I would argue against your point on progression. Shadowrun is based on a different system, while the level of D20 based systems, and MMO's, is quite obvious, progress in this will not be as obvious. It is much more determined by reputation than it is level and skill. Even to a degree items and technology that the player has access to are signs of progression, in comparison to before I can't hurt a kobold, to a full blown orc butchering whirlwind of death. Less tangible, absolutely, still present and still quite valuable if you're after that form of progress. In this I blame D&D for setting so much of the language and expectations in stone.
Furthermore, if you do impliment a set of achievements or use reputation as a method for tracking player's success, then you are in fact placing value on the type of style they play with. I don't see a way to separate the two. More importantly for a healthly base of NPC varieties, you run into those who value non-lethal solutions in comparison to lethal.
Also, while I appreciate the fact this is not to replace, but add to, the Shadowrun universe, it has to give due respect to the freedom of the PnP system. If I want to take the chance of pure disguise, this has to give the appearence of that freedom. Furthermore while you can't have a face path, social skills will have to give serious thought to make sure they are not entirely useless. If anything my suggestion in working down the path I believe you want to work, tying the skills into the preparation phase, in the form of additional contacts which can be used, as second tier set of contacts. Instead of just getting the layout of the security system, a grace period for the player in which it's being 'upgraded'.
I imagine that due to the technical complexities of personal player housing, that it's more on the long term. With the suggested launch, unless you want a very late 12 release, I can't see how such a complex additional feature could be fully developed and tested. Of course, see above point on my own work.
Nevermind you want to give them the freedom to have choices, from the previously mentioned lofts and abandoned/condemned buildings to high class inner city apartments. I feel sorry for your art department.
50 million USD to make a client based MMO? Should I start fund raising now?

Firstly I think that if such an approach was done, the money should not be too hard to acquire. I would think that with the maturity of the MMO market, more importantly the focus on fantasy, it should not be too difficult to enter some form of partnership or other commercial relationship. While I am not an avid MMO player, primarily the titles I am aware of are fantasy based, or as with the rating I saw given to Star Wars, low level fantasy. EVE Online and Star Trek Online are the only ones to really break the mould.
What you have a unique setting, with elves who can have sniper rifles, trolls with assault cannons, dwarf hackers, orcs wielding two fire axes and plenty more besides. I think more complexity is coming from the fact melee is valued equally with ranged combat, as this is a fundamentally lethal setting on the grand scheme of things. Chunky salsa is a prime example of this. I can't see why, with the focus on a particular setting that getting the financial support for a larger, client based end product. More importantly keeping with the isometric view, in comparison to a full 3D world. Not only would this set the world apart, it would keep the technology requirements, which is important for the MMO. Nevermind I think some of the best CRPG's are isometric views. On top of that a certain retro styling has always worked for this game.
I suppose there is an odd state in that you are both competing with, and not competing with, WoW. You are, in that it is the most successful western established MMO, and you are not, because you're running (wish I thought of a better word) a different end product.
If I had the link I would refer to it, because as long as you want crafting, you need the player base to see other players, which is how Memory Alpha and Lord of the Rings Online have it structured. I don't think there is anyway to change that, from your side of it.
I also think I should have the freedom, should I so choose, to create a 5'8 busty(female) red headed character assassin who chooses to not kill people, or a 6'0 blonde blue eyed male, angry shooter that blows through the guard force. At this stage I have to say it looks like I will need to find the right pen and paper game to give me the chance to be the character assassin, rather than just assassin. It's the curse of electronic games, which I believe you can work towards removing with careful, well thought out background systems. Technologically you're not facing the difficulties that many other studios would, so I can't see why a focus on characters(players) in a very freeform world can't be the core of the design. So far it seems to be more on the consistancy of the world, which is not to be overrated, but not the core. Especially in a classless system.
So.... at least I have given you some ideas, so hopefully I might get a mention or two in the office over the next week. Don't suppose I could get a reference for my resume for the next design position I apply for?

Finally something you might be able to use, for some Matrix interaction, perhaps basing player trading on a Matrix system, foci on an equivalent Astral system, with a screen to represent the different environment.