I'm a little worried the flask plugins are thin. As with anything where you have lots of flexibility, you can stub your toes if you don't know the "right" way to do it. For example, I tried to use flask-assets and pyscss to compile sass, but I found a bug in pyscss pretty quickly and had to back out and switch to the Ruby implementation of sass. Not ultimately a big deal, and the whole thing was up and running in about 3 hours.
EDIT: Ugh, more pain with Flask plugins. Flask-SQLAlchemy assumes you're going to declare models that won't be used outside of the web context ... so you can't separate your models from Flask. Annoying! Getting fixed here: https://github.com/mitsuhiko/flask-sqlalchemy/pull/250
So, anyway, that's what I'm going to do! Thanks for all your input!