yes, native client doesn't support access to gamepads yet but they will add an API for this in the future.
i find this technology very interesting. it's operating system independent already and in the future it will also be cpu independent (by using llvm bytecode). all platforms (win/osx/linux, tablets, phones,...) could be covered with one solution.
it would be ideal for gamestudio but looking at the low activity on the beta features page recently i gave up all hope.
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i also think this is the end of flash. adobe's last hope for flash is to make it a strong technology for 3d-games but who needs that if something like native client is available?