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Just for grins, I gave it a shot. It doesn't look like there is anything really major wrong, just a few minor things.
I made an xhtml5+mathml document, which I fed into ebook-convert to create an epub. Calibre generated output that kept all the mathml in there, which was the right thing to do. When I viewed the output epub, the mathml couldn't render the math, but it gracefully degraded, which is also the right thing to do. (E.g., superscripts just didn't show up as superscripts.)
As far as I can tell, there are only a few minor tweaks needed to get the converter to generate epub 3+mathml output that would be appropriate for future readers that can render mathml:
There needs to be a command-line switch to tell it you want epub 3 rather than epub 2.
When that switch is set, it needs to write xhtml5 rather than xhtml 1.1, set the mime type to application/xhtml+xml, and write output files with extension .xhtml.
The mathml property of the manifest item element should be set if there is mathml in the document. That can be done regardless of whether the user sets the switch requesting epub 3.
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