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.

I meant the user interface, but yes it would probably be possible and have benefits. It is going to be only 1 level though, it's how we built the architecture of the game and also ship-to-ship combat would be problematic with multiple levels. Especially when we still want the possibility to combine ship-to-ship combat with crew combat. On multiple levels set-up you would have your crew fighting on different levels and then fires, explosions etc happening on others. Combine this with having to pan between different ships/station and it would become way too much to keep track of.