It's not just about markers/journal. It's about "systematizing" game features, which is something many designers tend to overdo.
I find this trend has exploded since the popularity of MMOs took off with WoW, but it's been there before as well.
It's when you over-design and you help yourself by putting game systems in order, and you make your design into a blueprint formula. Bioware is probably the worst offender in the current AAA segment.
I HATE this trend, because it makes gaming very, very predictable. Even if you don't know the story or the characters behind a quest, you know exactly WHAT KIND of quest you can expect.
Having every single quest auto-logged in a journal with a precise quest marker to show you the way is a symptom of this widespread disease.
So, designers need to re-think how they approach design if we're to have any hope of getting back to the unpredictable "mystery" when playing a game.
I doubt this will happen, because it's much, much harder to have dozens of people working on something that's not systematized in some way. Modern development is about coordinating zillions of resources - and you need very clear stuff to point to during project meetings.
It's to the advantage of the indie developer, because developing solo or with very few people means you don't have to formalise your development or your design goals to the same extent. You can keep much of it as a surprise to the player.