Well, while I personally have a lot of love for the less...modern times of SR3, we are going to base our setting on the current timeline - heck, we are evn going to crossover stuff from ongoing PnP plots.
That being said, the 'feeling' we are going for is a bit less polished, more gritty, which was more what the SR3 edition was about, in my view.
Regarding rules - the conversion of many rules will sort of blur the rules distinction anyway and some things are just plain parctical. Take comlinks for example: Players will have the ability to chat in the game (indeed they could use any other chat program outside the game for that matter), so assuming everyone has a comlink pretty much emulates that part well. Same thing goes for AR - a wondeful way to overlay matrix info over the actual map layer, as opposed to jacking in somewhere and then being "alone" in the game from that point on as a decker/hacker.
I know rules are VERY important for the PnP - they will be slightly less so for our game, since we pretty much run it under different conditions anyway.