Rather than having fixed structures, why not let the player build however they want and then place objects to do what they need? So rather than having "barracks" you build whatever you want, put some bunks in it and call it a barracks? Or if you need an armorsmith you build a house, put a furnace and crafting table in it and command one of your units to make armor there? The more open the gameplay is the more it would benefit from using the minecraft engine. Otherwise it has nothing to offer beyond other RTS's.
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