I feel like a Danmachi X Nier replicant/automata crossover would be pretty good.
Like Popola and Devola are the ones giving out orders to the other's while planning for the shadowlord. Nier, Kaine, Emil, and Wiess are their own party, trying to find a cure all for Yonah, while she helps around the base to the best of her abilities.
We will still have 2B, 9S, A2, and some of the others being there, but most of the time, stay with their party members.
Project Gestalt is a way to basically live forever if done correctly, and Project Yhora is a way to stop the truth of the wrongdoings of the Familia they are technically in.
Shades would be on different floors depending on which shade they are. But depending on the circumstances, find a way to go onto the lower floors or just somehow get upgraded to something that would be on a higher floor.
I don't know why this came to my head, but once I get the other stories finished, I may do this.