The problem with having certain kinds of threats is that the setting has evolved to the point that those threats are outside the scope of the campaign. As an example, I'll note a toxic shaman. The Draco Foundation pays a bounty on toxic shamans; I think the going price was a million nuyen, but it could easily be only 100,000. Even a hundred K is beyond the payout limits of a Missions adventure. And there are groups out there that could handle a toxic shaman; all his toxic spirit buddies; and any henchmen he's got, and come out wondering why the job was so easy.
[spoiler]Case in point: last game I played, SRM03-04 Monkeywrench. If I'd rolled just a little better, my rigger would have stolen a Knight-Errant Hughes-Stallion kitted out for SWAT. And I was playing a rigger almost straight off the pregenerated character in the book. That sort of thing is way beyond payout limits for Missions, I'm betting.[/spoiler]
Now, IMR. While useful as a story tool, I find that its implementation can be used a lot better than using it as fiat for 'you find yourself in a bad situation, now you have to work your way out of it'. Here's the way it should be done: The story starts out as the runners find themselves in a common scenario; for example, on the way out of the mission. Say, they have Knight-Errant on their heels. Insert Flashback: They're at the meet. The Johnson has just laid out the mission. The 'runners have agreed to the job. (Well, if they don't, then they don't get to go on the mission, and I'm assuming that they're all there to play Shadowrun)
In fact, the whole job is a flashback, and they end up on the run (with KE on their tail) through no fault of their own: they were spotted and the cops were called. They then reach the point that the Mission intro started them at. Now it all makes sense. In this case you don't just say that they started in a bad situation; you let them get into that situation on their own.
And that's how you use in media res.
Deacon