I can really appreciate the ones that're designed to be woven in with your normal campaign arc - I feel that it gives the players a much better "A ha!" moment and general feel of design as opposed to a FOTM job (Not that I'm bashing stand alone jobs). It's a tradition in Shadowrun that dates back to the original Harlequin and besides - if there's something you don't like in one of the pieces, it's your game. Keep the element, or the purpose and change it to what you'd like.
I actually just picked up Sacrificial Limb the other day and have only just started reading it - which of the sections don't you like, and why? Or maybe I should ask, what don't you like in each of the setup adventures, specifically?
- Wailer -