This is fantastic, it feels like a must have feature for people wanting to play "campaigns".

Yeah, it needs to be flipped for the game to recognize that whatever villain is in that slot is actually defeated, and Bugbear gets a +1 from it. I've added it to the known issues.

One little comment on Team Villain mode- Boss Rush counts as a defeated villain, so Bugbear gets a +1 on all of his attacks if he's in play.

While this mod is very fun, people should be aware that it works primarily in singleplayer and many of the bosses will simply desync in multiplayer and lose their setup. This is particularly bad with the Ennead, which will just give you an instant win since none of them come out, and heroic infinitor will have his crushing cages, which is pretty horrible having indestructible crushing cages on heroes. I haven't encountered any problems in singleplayer though, and it's quite fun planning for longer campaigns and getting to know hero decks really well.

This is incredibly creative, thanks for making this!
Is it possible to also make it swap environments as well, and/or to possibly implement a rolling roster change of the heroes? (so each new match, one hero would be replaced, thus over time your team would slowly change)
Anyways, this is a really fun twist on the normal gameplay and I really enjoy it.