Is there a way to make MediaElement support more video codecs like mkv, flv, mov etc.? If not, is there any other control that supports more video codecs?
Have you seen the Player Framework? It's an open source component supporting Windows 8, part of the Microsoft Media Platform, and developed by Microsoft. It's an alternative to the standard MediaElement control, and provides a plug-in mechanism. I'm not sure whether you can support extra codecs through this mechanism though.
Other than that, you can also extend the media platform (the extension has to be written in C++ though) as shown in these samples provided by Microsoft:
The second example is very interesting as it's a sample media extension adding the MediaStreamSource mechanism as in Silverlight. Thanks to this extension you could implement your own MediaStreamSource in C#/VB.NET providing content to the MediaElement.