I remember my kids playing Minecraft at 6, the exploring and the building like the article describes. But by 8 they had discovered the 'other side' of Minecraft, the servers that turn the world into a low-res version of a PvP game, and most of the 'building' went out the window.
My greatest times playing together with my young sons was had not in Minecraft, but in Age of Empires II (vastly preferred by all over I or III). Usually we'd play us against the AI, and they got pretty good at it so we'd sometimes play against each other as well. I think the RTS genre holds more potential for a common ground between parents and kids than either the 'virtual lego' or the FPS categories.