Hmm, you neglected to mention what I personally think is the most important difference... GameJolt is 100% about games, Itchio lets you sell stuff like game assets, digital books, and even physical goods. So itchio basically is a marketplace for everything, so all kinds of indies can use it, not just indie game developers. AFAIK it's pretty much the first place that does this in the west, which is really cool~
(and yeah, I'm a bit biased here since I do game assets more than I do games nowadays... sorry about that :P)
Also, having used both: Itchio is much easier to use - it feels like every workflow and menu in GameJolt has a few extraneous steps added for no apparent reason, and you basically need to have a guide open in another tab to get ANYTHING done because a lot of stuff is so obtuse. Itchio not only has easier steps for everything, most of them are optional.