my main game is still running so i'll have to be sparse with the details (they play pbp here!)
I had a concept of a really bad guy/organisation in my head and thought up his/its motives; where it was based, what it was trying to achieve, and the various alliances and enemies they made along the way.
I started off with each of the players doing a solo run that happened to involve some part/element of the bad guy/organisation and then brought them together as a team under a johnson in act 2.
I have an idea of where it'll go, it needed to be quite proscriptive in act 1/2 to set the scene but act 3 is going to be a lot more open ended. the players loosely know that they're working for someone against someone/something specific but dont know what/who/why at this point. it's all starting to come together though :-)
to be honest mate, i get the ideas that shadowrunners take on whatever job they can to pay the bills. they may not get involved in long term campaigns against the same organisation all the time. they do the run, take the pay and go home all being well. if your players are happy doing one-offs, stick with it.