For the campaign I'm running for my wife, Brie, the action is taking place in and around a single large city. The city centerpiece is nice since if offers the potential a ton of factions and recurring NPCs in one location. But if I keep the action in and around the city, then it gets hard to explain after a while why there are so many tiny dungeons within walking distance.
So I'm taking inspiration from a variety of people who have designed megadungeons by stacking up a bunch of mini-dungeons together in one way or another (e.g. John Arendt's, "Design Principles for a 5E Megadungeon," KJD's "Node-Based Megadungeon," David the Archmage's "Mini Dungeons and Mega Dungeons," EdOWar's "Example Mini-dungeon Map").
Based on their ideas, I'm making my own Black Tower dungeon in a similar way simply to justify all the mini-dungeons in one place.
On a macro-level my Black Tower megadungeon will be ridiculously easy to navigate, with each level being a very, very long, straight corridor spoking off from a single entrance, with numerous branches leading to nodal clusters of rooms, each of those being in essence a mini-dungeon of about five to ten rooms. A level looks something like this:
Each hex represents 500 feet, and the black hexes are mini-dungeons. With five to ten rooms per node, and roughly fifteen nodes per level, each level will effectively have over 100 rooms.
I think that the way I'm doing this isn't a true megadungeon, not in the way, say, +Ken H's (most excellent) Montporte is. In the Black Tower, there is no real navigation or exploration, no significant backstory linking the whole dungeon together, and the nodes don't really connect directly to each other (though I'm thinking some may, via secret passages, teleporters, etc.). In the end it's just a way to have lots of possible dungeon adventures in close proximity to each other.
Factions in the dungeon may be allies or enemies with each other, but it's more likely they'll be allies or enemies of factions in the city. So the game will be a sort of half-city-half dungeon campaign, where dealing with things in the city will often lead to delving into a specific part of the dungeon, and vice-versa.
I think this setup will let me both play to my strengths as a DM and to Brie's preferences as a player. Win-win.