Quest markers only work if you have quests designed to be solved in one way and run through in a linear fashion. If the game is designed without an explicit quest structure, and multiple ways to do things, it isn't quite as good of a fit.
A better journal could help with things like getting back into the game after a break, though.
But a better journal would also need some kind of way to at least show where we have to go. (If we have to go somewhere, for a quest) I would already be happy just by having a floating ! above an area or something which is only for that quest we have "active" in the journal as active quest.
You are of course right that fancy quest markers can not work for a game where.. everything is possible. But general ones, specific to the active quest, that at least show in what area a button is, where we have to next and what is relevant to that quest. Such stuff would be nice. (Also for inventory items -> quest items should (optionally!) say for what quest they are ,p)
Such little things of ease of use features would have prevented me from stomping through level 16 enemies as level 12 party of 3. Was very challenging... ;P Explosive barrels ftw. I think I used up any explosive barrel In the entire cysael area I could find for my eplody traps in the forest...