We actually didn't really get any negative feedback about this scene at Origins or Gen Con. I think most players realize it's just a cut-scene to set up the adventure. And hey, even the most bad-ass experienced characters end up unconscious through no fault of their own at some point.
The big outcry with the earlier version of 03-09 was a combination of things... 1) That you didn't get the chance to negotiate your pay. 2) That you willingly Laesed yourself and let someone else set you up in a closet. 3) That you were supposed to jump in and go metaplanar hopping for no additional pay. 4) Due to the metaplane thing, some characters were limited in what they could actually do, especially in the earliest dafts that were run at Origins/Gen Con 2009.
With 03-12, while In Media Res isn't perfect... <shrug> It's a storytelling device. The players are never "out" anything, really. You still get the chance to negotiate for some big money (and stock options), you get your stuff back pretty early on, and you roll from there.
And yeah, that fight at the clinic... It's not nearly as tough as it could be, but this depends heavily on the group. That fight would be really, really nasty if the runners don't have a mage, for example. It's not really supposed to be all that tough. Plus that adventure had some time constraint issues that cropped up.
All in all... It's a big, wide-screen style season finale. It's big on story and action.
Bull