The minimalist nature of Flask, not forcing you to do things in one way and one way only, gives lots of power, but also lots of chances to mess it up and end up with a totally unmaintainable crap. Great power comes with great responsibility. Personally, I quite liked https://github.com/mattupstate/overholt (although some dependencies are out dated!). Also, having some starting point with the boilerplate code already in place helps you to prototype faster, etc.
Speaking of modules, the Flask modules ecosystem is pretty great and familiarizing yourself with it might save plenty of time you'd spend on re-implementing them. Some popular modules that are worth mentioning:
1) Flask-assets https://flask-assets.readthedocs.io/en/latest/ allows to easily integrate processing of the assets (JS minification, SASS compilation, etc) into your development pipeline;
2) Flask-login https://github.com/maxcountryman/flask-login simple users management (roles, authentication, etc.);
3) Flask-SQLAlchemy http://flask-sqlalchemy.pocoo.org/2.1/ simple integration with SQLAlchemy
4) Flask-Script https://flask-script.readthedocs.io/en/latest/ makes it easy to write command line tools which run in the context of Flask application (e.g. some cron jobs).