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MobiPocket is without a doubt the most widespread and popular format out there. Pretty much every device on the market, except Sony, supports it. I have no idea what I'll be reading my eBooks on in 5 years time, but whatever it is, I am entirely confident that that device will support MobiPocket.
There's no reason to suppose that Amazon's ownership of Mobi means anything other than sound financial support for Mobi. Bear in mind tha the Kindle is US only; Mobi sales are world-wide. The Kindle is entirely irrelevent for the vast majority of us.
ePub is technically a lot more capable than MobiPocket, but for novels those additional capabilities are pretty irrelevent. Most novels don't require complex formatting.
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