I think it would be very difficult to create a game that captures the feel of Shadowrun. Sure, you could create one that reflects the rules just fine. You could even make room for player run corporations and give it things to do that involve recruiting other players as deniable assets (ie Shadowrunners). You could build in skill learning times that are always ticking to give casual players the same skill growth curve as hardcore players. The old Cyberpunk CCG had some great ideas as far as abstracting the Corporations' operations.
At the end of the day, though, Shadowrun isn't about a classic hero's journey, at least to me. Contacts by themselves do a lot to change the average Shadowrun game into something more immersive than your average dungeon crawl. All of those great NPC's and plots would either have to be automated, which flattens them out and takes away a lot of the impact, or run by a dedicated NPC team, which would be hideously expensive. Even with player creatable corp plot, it tends to be reduced to game mechanics. Look at the big EVE Online corporations and you'll see that their politics have more to do with player interaction than character interaction.
Once you reduce Shadowrun to the level grinding button mashing of most MMORPG's it becomes just another face in the crowd of a genre that can't hold my interest. Ymmv
Edit: And don't get me started on what Shadowrun would be like if you could respawn a dead character. A world where everyone is effectively immortal would have some big diferences that most MMO's don't bother to account for. Even if Doc Wagon makes it in time, the consequences of getting hosed in SR should go beyond waking up in the hospital with less money.