The difference is that fast travel (to most location from the start) will always be optional, while quest markers in combination with a lack of journal will always be enforcive (at least in a big game world).
Problem is when developers start designing world and quests with fast travel in mind.
There is really no need to hand design every area in the world and carefully place recognizable landmarks to provide direction when you can just fast travel anywhere.
There is no need for preparation for a long trip since you can just fast travel.
Why not just put bunch of quests that need you to backtrack from one to another part of the world when you can just fast travel.
One of joys of Morrowind was finding those shortcuts and best paths to your destination. The world felt like a puzzle to solve and there was a sense of accomplishment when you solved that puzzle.