I'm also a Flask user, and I honestly don't see anything that might cause alarm, though I've only scanned the code so far.
In fact, it looks much more structured than the majority of my own Flask apps, but usually, by the time an app gets to the size that this already is, I'm either moving or considering moving it all to Django.
Actually, yeah, I take it back. I don't know that I'd swear it off altogether, but the INSTALL document is really quite convoluted.
While I appreciate the author's statement on avoiding SQLAlchemy to create models, I know that it can be done, and generally, that's what a person looks for from a framework like this -- to get the fiddly bits right.
It might work or it might not, but it will definitely take awhile, and the comments in the INSTALL doc are seriously snarky.
Sure he had fun with the install doc but it looks complete. I would much rather have some snark and complete instructions than an incomplete quick start tutorial.
In fact, it looks much more structured than the majority of my own Flask apps, but usually, by the time an app gets to the size that this already is, I'm either moving or considering moving it all to Django.