I think the biggest difference is one of philosophy: in Fossil (as I understand it) every change you make to the code is tracked, and there's no concept of rebasing or making the history prettier. If you make a commit and then realise you've left some debug logs in the code, you've got to make a new commit to delete those logs. This has the advantage that you never lose data, but the disadvantage that all of those commits end up in your long-term project history, making things like bisecting or blaming more difficult.
In JJ, however, changes are explicitly mutable, which means if you finish a commit and then realise you want to go can and change something, you've got multiple ways to squash your fix directly into the original commit. In addition to this, you also have a local history of every change you make to your project (including rewriting existing commits) so you still never lose any data locally. However, when you finish adjusting your commits and push them to someone else's machine (e.g. GitHub), they will only get the finished commits, and not the full history of how you developed them.
I know some Fossil people feel very strongly that any sort of commit rewriting should be banned and avoided at all costs, because it creates a false history - you can use Jujutsu like that, but it probably doesn't add much over Fossil at the point. But in practice, I think Jujutsu strikes the right balance between allowing you to craft the perfect patch/PR to get a clean history, and preventing you from losing any data while you do that.