I actually like Django's querysets a little better than SQLAlchemy's, but most other things better in Flask. I may be a heretic.
The declarative API in SQLAlchemy requires much more work to set up relations, and the Django way of being able to chain relations in a query with "__" is pretty friendly in ways that I like.
I recently created a new API and went for a very simple flask.Methodview along with Marshmallow [0] for (de)serialization. I then wrote a simple replacement for marshmallow-alchemy since it wouldn't do object loading without a lot of flapping about.
I found Marshmallow really nice to work with (I'd been using Schematics in the past).
I've been kicking around different approaches to this for over a decade, going back to Castor (Java data binding), and with Python, SQLAlchemy, and the libraries mentioned here I'm finally feeling optimistic.
Request parsing in Flask-RESTful seems bolted on, and the fields in WTForms seem frustratingly redundant given that almost everything I do is going through the API anyway. Maybe focusing more on the Fields themselves will help tie it all together.