A few things that might be useful in novels are:
- Drop caps.
- Embedded fonts.
- Images with text flowing around them.
- Scalable vector graphics (SVG) allowing you to have graphics which look good at any resolution.
- Much more advanced table-drawing capabilities than Mobipocket is capable of.
Unfortunately the very flexibility of ePub is also, in a sense, its weakness. As I mentioned above, NO reader fully implements the ePub standard, and different ones implement different parts of it. This can make it difficult to produce an "advanced" ePub that renders well on all devices. ADE-based readers, for example, support different ePub features than the iBooks application does.
There are features of the ePub standard which no reader yet supports. One example is "page-based" display elements which should (if they were implemented) allow you to have proper footnotes in a book, appearing at the bottom of the page in which they are referenced, just as they do in a paper book. Unfortunately no device yet implements these.
Mobi is a decent enough standard for the typical novel, which is why I'm more than happy to read on my Kindle, but there's no doubt that ePub lets you do far more "advanced" things, and that's important when you need more complex layout, as in textbooks, for example.