Where PWA is not the best choice?
PWA technology can be used in a wide variety of cases. But as every technology it has its pros and cons. It is very helpful in getting into smartphones and does wonders for customer self service apps, but there is a range of applications where PWA tech is not such a good choice. Remember that PWA is based on browser capabilities, so anything doable in browser is a good choice for the PWA approach.
Making any kind of games, but the most simple ones. Limitations of browsers and java scripts.
Virtual and Augmented reality
These apps require a lot of computing power and a careful management of smartphone's hardware
High animation apps
This is an arguable point as animation is possible in PWA, as it is possible in a browser, still you need to evaluate your decision to employ PWA case by case. If you go for PWA in this case you must consider keeping away from any app making platforms, but rather go for fully custom make code in any IDE and relevant frameworks.
So in general applications requiring lots of deep and carefull hardware work are better of native. PWAs are very good for various business processes apps, service apps and other cases requiring speed, simplicity and user base coverage.