I was using an MVC style structure for one of my sites, but have recently changed to a module style structure.
For me, the change was for pushing to production reasons. In an MVC style, you could push individual files from different folders to production, but with a module style - I know what ever is in that folder, belongs to that module - so I just need to push that folder and be done. No concern about pushing an incorrect file or overwriting something that shouldn't be.
Neither is right or wrong I don't think - whatever works best for the project at hand.