I remember the first time I played Baldur's Gate with the expansion, I neglected to read the manual or any guides and ended up going to Durlag's Tower fairly early on; the upper part of the tower wasn't all that difficult, and I managed to complete it as I found it. The lower portion however I didn't even discover at that point. It wasn't until I got to Ulgoth's Beard that I figure out that there was an entire ****ing dungeon underground. And even at that point I wasn't quite the level for "proper" enjoyment of the dungeon. But I got through it anyway with lots of trial and error, and got some items that were overpowered at my level range (which is absolutely fine, I like being rewarded for getting through stuff that I'm not at the proper level for).
So, bearing in mind that some people probably aren't as stupid and unobservant as me, it could certainly be interesting to have a dungeon that is divided up into individual sections, some parts even being above ground, like Durlag's Tower, with multiple entrances - with different parts perhaps related to different quest lines outside of the dungeon. They should still be accessible without having to go through the quests, but I mean just as a way of introduction (another example would be the Super Mutant Base in FO1: you could have the Brotherhood quest take you there, or you could accidentally stumble into it (as I did...right after leaving V13)).