However, my opinion is that is a PITA that every Flask project has a different structure, unlike a "batteries included" framework like Django, Rails, etc.
Most nontrivial Django websites also have varying structures. At least they did a decade ago when I was working as a consultant specializing in Django. About as much commonality as Flask. Did Django ever figure out a less verbose way of declaring REST APIs with arbitrary serialization?
I agree. Flask is quite nice, as are some of the other things based off it, like FastAPI, and some of the Flask-inspired async frameworks, and the Jinja template engine that Flask uses. All good stuff.
However, the focus has moved to py4web [1] which has many of web2py's strengths (including the DAL), but with a more orthodox architecture at the cost of a little more complexity and a slightly steeper learning curve.
Stuck for a while in python 2.x world with its "always backward compatible" pledge... then it lost attention I guess. Also, questionable technical choices. Now py 3.5+ compatible, but no compelling reason to use it.
However, my opinion is that is a PITA that every Flask project has a different structure, unlike a "batteries included" framework like Django, Rails, etc.