I personally think each of the challenges are well thought out!
Favourites: Badder Bosses and Swarm Intelligence. These imho add a nice layer to the game.
Least favourite: Into the darkness, it annoys me getting sniped from a ranged enemy without seeing anything.
Special shout-out to pharmacopoeia and faith is my armour. I cannot finish the game with these on - anyone got any tips?
As a Huntress player who relies on range and grass cover, Darkness and Barren are the 2 I dislike the most (though I could deal with them in a low chal run). FiMA can be rough but it teaches you a lot about avoiding damage, similar for Pharma where healing is at a premium especially time-wise.