I can sort of see slight Gary Stu aspects in retrospect (always taking into account that I don't know the man, so I can't really say if it resembles him at all), but I usually give authors a pass on that and don't really look for it, at least if they're writing their own works (rather than fanfics, etc), since there's often a fine line between Gary Stuism and the combination of "write what you know" and "make a compelling protagonist" (which usually means having a bunch of stuff which, if you applied it to yourself in a fanfic, would absolutely make you a Mary Sue). Actually he kind of failed on the latter part for me, he wasn't terribly compelling, but I didn't find him annoying either, he felt like just a vehicle to get through the story.

But yeah, Accelerando was much better. It's a shame Stross seems to be interested in writing more Laundry books but has no plans for more far-future/Singularity ones.