I think the series started off on a strong premise but it kind of got off the rails for me further down. It'd be interesting to see how Fabletown would have to be tailored to fit in the main universe though.
I agree on the strong-premise-but-went-off-the-rails bit; it sort of peaked (for me, at least) with the end of the Adversary stuff (
I'm trying to keep it vague, so as to avoid spoilers, just in case!). The stuff that followed became hit and miss, though there's still some really nice bits in there. I've got my fingers crossed that the spin-off-ish series are closer in style to the earlier ones.
Anyway, before I get lost in trying to work out when, exactly, the series started to lose it's way, I'll go away and think of how one might go about fitting Brock in. As for how it'd fit into the main universe - it's already established that there are many worlds, and that stories / myths / legends told in the Mundy world of Fables tend to be reflections of these worlds. In the Super Team bit, they do try to tap into the power of comics, and so it doesn't seem like such a stretch that, from the perspective of Fables, there exists some comic book inspired world populated by super heroes, nefarious villains and what-have-you. It'd let you cherry-pick a little in terms of how much stuff from Fables you'd want to see more easily, presenting it (again, from their perspective) as another world amongst the many, rather than as the world that the exiled Fables chose to retreat to.
Or, of course, Fabletown could just be plonked down somewhere in Metropolis, and tie the whole thing together that way, but it'd probably require a fair bit of fiddling to make it work without breaking the "feel" of things. I'm more than happy, of course, to go with whatever option you decide would work best for your game! There are plenty of ways to fit the Fables in, I'm sure, and perhaps we could muddle the continuity up such that it keeps that sort of "Legends In Exile" theme that made the early Fables stuff great. Also, um, apologies for the wall of text.