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My quick fix is to use naming of media type classes to "tell" EPiServer what is the default one. Would be great if there was a better solution for this - such as using an attribute of some kind.
A solution to the problem:
http://geta.no/blogg/resolve-default-media-types-in-episerver/
In my solution I have several media type classes that will match for jpg/png using MediaDescriptor.
Is there a way to tell EPiServer what is the default type? Looks like EPiServer simply picks the first type it finds.