Maybe some developers will create some more capable media player ATV apps, like VLC, if they're able? But it's probably too soon to say right now.
In the meantime, Beamer for Mac works really well for "air playing" avi and mkv and other movie files over to the Apple TV. And Subler works really well for quickly converting mkv into mp4 files (it only needs to covert the "container" for mkv files because they and mp4 files share the same x264 codec, so it's not too intensive or process-heavy a conversion).
So those are the two options that I currently use that work really quite well.