Of course you can use any number of ways to implement rich text or formatting. A lot of people want Markdown because of the portability of plain text. Markdown has served as a good mechanism for plain text formats that still can do a bit more. Ulysses would lose a significant portion of its audience if it moved to it's own syntax or some form of rich text or its own binary. A new audience would likely become interested-- though fighting Microsoft Word is ... hard to say the least.

Maybe that's where Ulysses wants to go, and its own implementation of some non-standard elements suggests that. But I also know people who will not use Ulysses because of its non-standard Markdown elements resulting in files that are less portable.