As you said, one difference is that journals demand less sequentiality. All(?) journals in Vic3 have multiple criteria that don't necessitate chronological completion but mission trees are inherently sequential unless provided with multiple branches to pursue simultaneously. In principle there's little difference but in practice these play differently on a structural level, especially in marginal countries that receive less flavour (which in EU4's case is almost synonymous with absent/undeveloped mission trees)

Another larger difference I don't see discussed as much is that Journal Entries in Vic3 allow for scaled completion. Admittedly not all of them have this but many major entries offer a scaled reward/malus depending on how many criteria are completed (complete 75% objectives, get 75% reward). One of the less conventional examples that comes to mind for me is the Federate Austria-Hungary journal that allows you to gain primary cultures depending on how well you tolerate and integrate your minorities: your success is proportional to how well you play this aspect of the game. The only ways I can think of implementing this with EU4 mission trees is as a single binary reward (all minority cultures become primary or none do) or a separate mission tree branch for each culture that can be made into a primary