Questions

Hey!

Decks would be possible in a way, but we might refrain from having them. It becomes hard to let the player know what
is going on, on each deck.

For example: If things are frantic on many decks, how does the player shift through them easily and give orders?

Even though going by the assumption that the players are complete idiots usually helps sales, i don't think it is a smart move if we are talking about small indiegame. We can assume they are made from sterner stuff.
There is no problem with Z-axis on dwarf fortress, so i would not think there would be any in this one either. More freedom and possibilities for micromanagement is always welcome.