That doesn't answer the question, mine at least provides structure in which the player must choose a side in the scenarios, like the companies we have now.
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Make both options.
Dungeons, which you can only enter after you finished a 10 hour story quest and story quests, you can only starting after you speaked with a npc in the deepest level in a dungeon.
If it's a choice, definitely story driven.
I highly doubt the dungeons would just be 'Here is a dungeon, go rank up!'. There is likely to have some story to them. In the letter it says the vangards of the grand companies were going to scout them out. Access to them may probably include grand company quest involvement, with quest chains and what not that lead into these dungeons.
This.
SE added the hectic weather, Guy preaching about incoming doom/chaos, and people get hyped. Now we get mid-high level dungeons and people complain about them being like WoW and not story driven...
What do people think the guy is preaching about? It may not be the start of the 7th umbral era but it's building up to it.
I remember reading some quests stating the people shadowy figures are hiding away in caves and whatnot. I believe it was my first LL quest that said that and I had to go to a copy/paste cave to kill a few.
Current option: bots driven.