Though I don't think the fact he's worked at exclusively big clubs detracts from his achievements, I do think it will ultimately be taken into account when it comes to judging the all-time best manager
Compared to Ferguson, who earned his chops at Aberdeen turning them into a powerhouse both domestically and in Europe whilst having to deal with the two Old Firm giants before getting the Man United gig, he's had a much easier time of it
That being said, the expectations of managing Barcelona, Bayern and City are way and above what Ferguson had to contend with when he was managing The Dons, so that deserves consideration also
There's no doubting that Guardiola is an excellent coach though, he just doesn't have a Porto or Aberdeen to his name like Mourinho or Ferguson do. Barcelona B doesn't count IMO, because it's youth football. Yes, it showed he was a decent coach, and yes he was playing senior sides in the second tier, but again he had perhaps the best youth project in the world to work with. He has never had to start from scratch, even though Barcelona weren't champions when he first took over. He still had a squad most people would be envious of