The Toptal.com blog has a tutorial posted by Elvira Sheina showing you how to keep a framework project "slim" and manageable in a MVC pattern using a "layered" structure. This structure adds a few extra components to the traditional MVC design to keep functionality cleaner and easier to maintain.
Fat controllers and models: an inevitable problem for most large-scale projects based on MVC frameworks such as Yii and Laravel. The primary thing that fattens controllers and models is the Active Record, a powerful and essential component of such frameworks.
She starts by talking about one of the main issues in MVC applications - "fat" controllers. In this example the controllers contain the bulk of the logic for the application making it difficult to modify and potentially reuse in other places. This is particularly bad when the Active Record pattern is used and the problem of it violating the SRP (Single Responsibility Principle of SOLID development). Instead she promotes the idea of the "layered" design using controllers, a service layer, DTOs, view decorators and a repository layer. She then shows how to implement this kind of structure and tie each of the pieces together with code examples for each piece.