Shoehorning everything into MVC because it's the "one true way" is where the problems arise.
My current system uses Controllers, Views, Services and Repositories with ORM objects as the "entities" (it's based on Laravel/Eloquent) and I've found that to be an acceptable trade off for the domain I'm modeling, MVC would have been painful when you have a lot of business logic.
Shoehorning everything into MVC because it's the "one true way" is where the problems arise.
My current system uses Controllers, Views, Services and Repositories with ORM objects as the "entities" (it's based on Laravel/Eloquent) and I've found that to be an acceptable trade off for the domain I'm modeling, MVC would have been painful when you have a lot of business logic.