If you reach the point to have a complex management of a multi-floor level situation it will be of course the best solution 
Anyway, I want to ask you a question: is your system ready to put some custom logic on cell adjacency?
For example, in my project I want troops joining together (or have symbiosis) in a special 3x3 formation when they are close enough and act as one big troop with increased stats.
Is it possible with your system to calculate adjacency efficiently at any time?