SQLAlchemy is great for certain classes of applications but rarely are the advanced features needed for web applications. It's one of the few things I dislike about flask development in general. It's the standard ORM to roll with flask and compared to Django's ORM it's WAY over complicated. Flask and a NoSql db is a dream though.
SQLAlchemy's documentation makes the ORM seem a bit unapproachable, but Flask-SQLAlchemy does a good job of simplifying things: http://pythonhosted.org/Flask-SQLAlchemy/. With that documentation I don't think SQLAlchemy is much harder to use than Django's ORM.
I think SQLAlchemy's documentation is actually pretty good; it's extremely thorough. SQLAlchemy is also extremely well designed/written (as is Django), though it tends not to hide its complexity. SQLAlchemy's sessions are more complex than Django's equivalent. This is because SQLAlchemy assumes a more general case, where as Django assumes you're making a standard CRUD web application. They're both good at what they do.
