I am wondering if anyone has endeavored to create a plugin that creates better video support in Omeka? I'm aware of the existing HTML5 video plugin, but wrapping video in an HTML5 video player is useless if the video it is wrapping is not in a browser friendly format – not to mention that even if one were to pre-process all videos, only having one format embedded would not be cross-browser compatible.
Doesn't seem like it would be much of a stretch to leverage ffmpeg for videos, just as ImageMagick is for images… just hoping someone else has already done the work.
I'm not aware of anything that currently does automatic transcoding for videos for Omeka uploads. You're right that the process is basically analogous to the existing ImageMagick thumbnail derivatives. For historical reasons, Omeka's core file derivative support is focused on images only, but there are some proposals around to change that.
I will note that H.264-in-MP4 gets you pretty darn close to native cross-browser support already, and the reason behind using MediaElement.js for the HTML5 Media plugin is to allow support for formats to be filled in for the outliers with Flash.