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Removing Dungeons from the Treasure is not a good idea. However, making Dungeons with heroes who don't have a Book would be a good idea. It would look more balanced – you couldn't say that someone just got lucky and a mage with a lot of mana appeared and destroyed the Center in one turn. Also, if I understand correctly, in the Center, you can only generate Dungeons with generic, simple Warriors, and with a pre-defined build – let's say all 20+ levels, all 8 skills at expert level (possibly 6-7, with empty slots, although 8 is guaranteed to be more balanced), and there are no Scouts, Pathfinders, Logicians, or Scholars (this eliminates the possibility of breaking and re-training).
P.S. Although, with the trading system for colors/castles, it seems strange to complain about the fate of the villain – learn to play, know your opponent, be honest with yourself and your opponent, and remember that the Game begins before the Game – how prepared you are, how you negotiated, how you anticipated all possible nuances – that will determine the result.