Botch the Crab has set together an online petition to send to Hasbro relating to bringing McDonough and Patyk back no matter who picks up the Transformer licensing http://petition.botchthecrab.com/
The Problem is I didn't care for their writing. Their stories dragged on and on and then gave very little pay off. They're good at characterization, but their plots sucked. 5 issues of Sunstorm led to nothing, and the Micromasters series was a big disappointment. Their best work was the Insecticons story, and even that was just an "Aliens" rip-off.
I would've liked to see a few more issues of G1 to wrap things up (and show some female TFs woo!) but on the whole I actually (gasp!) agree with BZ on this one. They came in off the boring TF guidebooks with the whole continuity already mapped out, but didn't do anything cool with it, and it boxed in what could be done in the sequels to the far superior War Within.
I did like their writings, and as riboflavin said, I would really like to see them at least tie up those loose ends left unravelled.
I think part of their problem was that they assumed they had all night and day to get the story told out there, so they took their time to do it.
As far as the guidebook, I'm assuming you mean MTME, and I LOVED those. They weren't perfect, by all means, but they were pretty good for what they were. They did a better job at giving personality guidelines for a SLEW of characters that we never got squat for before. I woulda loved to see their takes on the Beast Wars characters, or on Japanese characters...