Sure, the framework's way might not always be the best way of doing things but I prefer to just accept it and move on. It saves spending time debating, deciding, experimenting with different ways of structuring code, when it probably doesn't really make that big of a difference in the end anyway. Most web applications are really not that different from each other.
On top of that it prevents really bad coders from rolling their own in a really bad way. Remember when everybody was coding their own MVC framework in PHP?
As for C# not parsing JSON correctly, that seems more like a problem with a language or library not anything to do with frameworks?