I don't have much of any input on this, because I haven't experienced it yet.

I'm fortunate enough to though, that the old FBO school that I first started flying at before I joined the AF, is now a small scale academy. To me, that's great, as it still has the feel of a good small, FBO, but it has the power to produce and instruct like a larger academy. Best of both worlds.

I would go FBO though. As stated above, I think I'll have a little bit of the best of both worlds, and of course, the downfalls of both the worlds.