The campaign I play in (2 plus years and 9th level) experienced this. We all started out in the Sunless Citadel just doing classic dungeon crawl, then followed that with Forge of Fury. The DM then switched to player-driven stories, but the transition was... a little rough.
One problem is that most dungeons present a few obvious options. You can go through door A or B. You can search for traps or open the chest. Now obviously characters have far more options than that, but they can always fall back on A or B.
Once you start running a character-driven campaign, the choices may be obvious to you as a DM, but they are not necessarily obvious for the players. Our DM has said, in exasperation, "You can do anything!" which doesn't really help because it's not actually true! We still have limited choices, but the problem is they are not presented clearly.
Let's take the example of building and maintaining a fortress. As a DM, I might think that the characters will want to go back to that friendly town, or explore that canyon, or rebuild that ruin... But if I just ask "Where are you going to build your fort?' often players will not have enough info to make a decision.
I'd recommend planning out your character driven adventures like a dungeon! You can use a flow chart to prep some obvious A or B choices, while also giving players the freedom to choose their own ideas.
For me as a player, it would look like this:
DM: Okay, you said your character wanted to build a fort. Over the next few days, you see two promising sites. There's Friendlyville, the town you freed from goblins, and there's Old Castle, the ruins you found that magic sword in.
Player: What about those mysterious canyons we fought the lizardfolk in?
DM: Oh yeah, that would be a great location. However you're not sure it's entirely cleared of threats. To be honest, you'd want to travel to any of these places and get a lay of the land before building your fort.
Player (checks with others): Alright, let's start at Friendlyville and then go to that canyon.
And so on.
Oh, one more thing. As a player I've found that the way we play out decision making has changed with the scale of our game. We used to try to play out decisions in character ("Aye laddies, let's go through Door A!") during adventures. But when we transitioned to the more abstract time required for fort building, etc, it was much more useful to talk about what we, as players, wanted for our characters.
So we went from "I want to search the chest for traps" to "I want Sir Garbogool to find a secure location for his new fort."
Hope this helped!