Mobi is an unholy mess of HTML-inspired markup. I don't think anything else uses it, and it was designed to be rendered on incredibly constrained hardware that just doesn't exist anymore. It's OK to use a few megabytes of RAM to render a document now.
Using straight-up HTML5 lets them dump a bunch of code for proprietary rendering engines, I suspect. And it simplifies the Kindle fire and web-based / PC readers, where they can just embed an HTML renderer.
(Disclaimer: While I'm a former Amazon employee, I didn't work on or with Kindle. As a current Mozilla employee, I think HTML5 is pretty nice.).
(Though I am quite ignorant of the MOBI format that is being replaced.)
This also bodes well for taking web pages offline and onto dedicated reading devices, a la Instapaper.