Actually, there are some minor and very technical differences between ePub and MOBI that make ePub slightly better. But on pure text books or books with simple layouts, those differences are not noticed by the regular and common user.
The interesting point here is that Amazon has the biggest ebook market in USA and probably in the world. People can say that ePub is the de-facto standard, etc, but what really makes a format standard or, in other words, what keeps a digital format alive is the market and the people using it. If MOBI or AZW usage goes up because Amazon (or other ebook stores that keep selling MOBI in order to please Amazon's users) ePub will be dead in a couple of years.
Business and technology is about money, market and demand, not how good a solution really is. If something sells good or is popular, then is a good thing in terms of business, regardless of how crappy the internal implementation can be . Most of the time both are true (something sells good and is the result of a nice technical development) but the final decision are based on sales and what the users finally buy.