I found this post over on Above the Flatline really interesting.
How I’m Organizing My Megadungeon
The gist of it - establish multiple up and down connections as well as horizontal connections in the dungeon. Allow for some chokepoints, but otherwise give a lot of choices of movement.
That's something that doesn't exist so much in Felltower, which has a series of chokepoints. That was deliberate, since I needed to contain the players within areas while I built out the dungeon. But it's constraining on actual play, since it means those chokepoints continually limit choices, travel, and decision paths even after I've made the dungeon. It's nice to see someone understanding the value of a well-connected many-choice dungeon in three dimensions from the start.