If you have a tablet, the Kindle app is awful.
What exactly is your ax to grind with Amazon? The Kindle app on the iPad works like its suppose too.
That's the problem. It's designed very poorly and works that way. No fonts, huge margins, it's just weak and doesn't look good at all.
One really good reason to go with ePub is because it's a better format then anything Amazon has to offer.
I'm not locked into DRM. All of my eBooks have had the DRM removed. So given a choice, ePub is it. Marvin blows away the Kindle app. And there is going to be an iPhone version as well that will again blow away the Kindle iPhone disaster (err app). On an iPhone, screen space is precious, but Amazon doesn't care at all about usability.