I would say you're out of luck then. What good are those mkv files if you don't have an app to read them?
There are a lot of things I'm used to doing on a computer that I can't do on an iPad. Everyone has their examples of things that make X inferior to Y. Apple has shown that they can be successful by offering less of "business as usual" while slowly introducing new ways of doing things.
The only way to advance the state of the art is to let go of a lot of the notions of what we think a computer should be. Is rearranging toolbar buttons really going to bring delight to people around the world? How does this help the guy who is miserable at his job because he's forced to use a 10 year old PC running Windows XP? How does it help the person who lost all of their vacation photos because they downloaded a photo editing app that turned out to be a virus? How does it help a four year old that's learning to read?
I would say you're out of luck then. What good are those mkv files if you don't have an app to read them?
I have a really nice app to read them called Media Player Classic -- I just don't have an app to manage them. Writing apps to manage every single file type I have is very inefficient compared to using a general purpose file manager. You abstract out often-used code rather than copy-pasting it all over the place, don't you?
The only way to advance the state of the art is to let go of a lot of the notions of what we think a computer should be.
The fundamental definition/theorem/axiom/whatever of computer science is the Church-Turing thesis. We haven't come up with a practical notion of computability more general than that, so it is by default the state of the art. Following from that, I think a computer should be a real-life manifestation of a universal Turing machine -- something that can run anything computable (taking into account resource bounds but also providing all the resources it can) without being beholden to another entity. Anything less is an appliance, a toy, and is not fit to be called a computer.
Files without a dedicated application will be the exception rather than the rule. Movies, Photos, Documents, spreadsheets, databases, music, books; you will usually open in a dedicated application. It's not hard to envisage an improved UI for files that do not have a dedicated application: they could be presented in a view showing all the files that are not associated with a program, for manual association. From then on, the system would know which file types to present along with that application. In addition, it goes without saying that full access to the underlying file system should be possible for developers and those that need it (which will be a tiny fraction of the userbase).
It's a ridiculous idea IMO because when I want to copy 2 docs, a jpeg and an html file from one device to another, I'd have to open three separate programs in order to carry out the task.
With a dedicated file manager, you open the one program and do it all in one step.
How do I tell iTunes (or any other music player) to import some of the music on my USB drive? iTunes doesn't even allow you to do that with iPods...