Here are a few alternate rules that I think make for interesting variations on Professor Pugnacious, but that after playtesting we ultimately decided not to use. They make for fun changes, though, if you want to mix up your game.
Persistent Failure: Failure tokens, instead of going away at the end of the turn, remain until they are assigned. This makes cards with Failure a lot more powerful, which is fun, but ultimately fairly game-breaking.
Persistent Victory: Instead of putting your Victory/Defeat token on an enemy after beating it and then immediately gaining the benefit that turn, you may leave it there until you want the benefit, and then remove it-use other tokens to track this on additional enemies. This added a lot of book keeping for a not very big benefit to game play, and to really run properly would require a lot of extra tokens, so we left it out. Most players ended up forgetting to use it, or saving it up for a few turns and ending the game early. This combines well with Persistent Failure, though!
Cleaning the Ring: For a cost of 2 less than the card, you can pay to trash a card in your Card Queue. This lets you get rid of cards nobody is buying, and speeds up the game, but it also makes a “turtling” strategy of just getting rid of all the good cards viable, which annoyed a lot of players.
Massive Combat: You can fight more than one Enemy, or the same one more than once. This is just completely bonkers, but some people like it.
I’ll add more if I think of any or remember discarded rules from back when we were playtesting. It went through a lot of variation back then. I’m happy with what we ended up with, but sometimes it’s fun to try one of those variants just for a change.