There isn't anything significantly different between JotDown and Markdown functionality; at the end of the day, it's simply a syntax that turns plaintext into marked up output. I wouldn't even argue that JotDown is more powerful or has more features than Markdown; however, I would definitely say that JotDown has a few built-in advantages over Markdown.

Vanilla Markdown is/was very incomplete, Gruber wrote the spec in 2004 and the "base" version of Markdown reflects it. There are numerous modules that are considered essential for the "base" version in order for it to meet the needs of authors nowadays (such as super/sub scripts, tables, lists, underline, strikethrough, etc). Modern implementations often already build these features in (such as GFM), but my goal was to include all of these features in the "base" versions, and have even more features as add-on modules. I approached this from reverse and based JotDown on the current HTML5 standards. So while the escape hatch for Markdown was for the author to write inline HTML, most HTML5 features are build into JotDown; you can use stuff like abbr or spoilers with JotDown syntax, versus using inline HTML.

JotDown allows for custom containers and style/id/class overrides, which allows authors more creative freedom on what they're writing (Markdown Extra actually already did this as well), and it's technically possible to write a static webpage entirely in JotDown (not actually an advantage since standard Markdown allows for inline HTML, though you can't use ID and classes), and while I wouldn't recommend it, I see a use case for lecturers to use it in the future to author their teaching content. Overall, I would say that it lets your notes be prettier, and who doesn't like pretty notes?

This is more of a technical issue rolled with a personal opinion, but Markdown's syntax share a lot of characters. The symbol '*' is used for both bolding(**) and italics(*), while in JotDown, it's !! and //. Personally, I think that makes more sense, it just looks better to have them like '!!' and '//' since that's how I always envisioned the final output. Technically, it doesn't allow for parsers to know what you intended to write until you finish the text. In any Markdown parser, you would need to fully write **example** before the preview shows "example" in bold. In JotDown, writing "!!" is already enough for the parser to know you want the text to be bolded, and it'll keep bolding until it encounters another "!!". This isn't really a problem, but as someone who's used to syntax highlighting in IDEs, I really wanted a true live preview for writing.

Lastly, I had a real bone to pick with '#######' styled headings, so they're simply '#6' in Jotdown.

Overall, this was a very lengthy personal project for a product that nobody but I asked for. I had issues with certain things and I had the necessary skills, so I decided to make my own (sans the blackjack and hookers). That being said, I do hope it catches on and more people will see it like I do :)

Please don't feel like a troll, I think I need to rewrite the "why?" page, 'cause I just re-read it and it didn't feel like I conveyed a lot of useful information. But I hope I was able to here!*