TL;DR: ePub > Mobi, I do not support RAAS (reading as a service)
Don't get me wrong, I love eBooks, and I will probably buy a Nook or Sony Reader some day. (For now my iPad is a decent substitute.)
Why does the Kindle rub me the wrong way? It doesn't render ePub books. I think the ePub spec, though flawed, is a great tool that generally follows the spirit of Unix. It's just complicated enough to be flexible but is something that you can pretty easily craft by hand. (I'm in the middle of building a library that will make that a one-line command.)
Mobipocket, on the other hand, is an ugly format. It's binary. It's over-engineered. It's legacy. Mobipocket represents each book, magazine, or comic book on your Kindle as a database for basically the same reasons that Windows still uses the Registry. I cannot deal with such an ugly format or support an ecosystem that refuses to support better standards.
Side note: I will never invest in a proprietary book "platform" because, I like to own my books. And book "platforms" are the road to RAAS (reading as a service). Amazon doesn't have a great track record for making you feel warm and fuzzy about owning your eBooks [1]. Giving up physical books is something I might do. Giving up the right to read them when and how I want is another.
[0]: http://wiki.mobileread.com/wiki/MOBI#MOBI_Header
[1]: http://www.nytimes.com/2009/07/18/technology/companies/18ama...