I only get the chance to play the PC version, so this may change how I deal with certain decks.
Heroes:
-Actually, I don't think there's any hero that I can't work with. Some where a bit trickier than others, and needed a bit of training* before I got how they worked, specially Absolute Zero and Bunker, but that's all.
Villains:
-The Matriarch, due to how bureaucratic the video-game gets every time you kill her birds (which are many), with all those confirmations of damage and target and redirection and more damage and confirming more targets and which effect should go first.
...And that's it. There are some villains that I find more frustrating than others, but I have the privilege of being able to train against them with specific teams til I "get" how they work. Heck, I may even play more against them than with easier villains due to the challenge. I even like playing against Miss Information, when I feel like trying to solve her "puzzle" as efficiently as possible.
Enviroments:
Now *these* can be a problem for me. It's easy for me to feel like they are "getting in the way", even more than villain cards.
-Megalopolis: Too much "you can't do stuff for the entire round" cards. Especially hostage situation.
-Rook City: A no-no for most games. Only played when I feel like the villain is too easy.
-Mobile Platform: While others are frustrating, this one is too passive. Mostly it will just play cards to protect itself, then play minions to fix itself, then play a level to play more cards to support itself. The "plane falls everybody dies" card is pretty cool, though.
-Magmaria: Like it was said, too little in the way of crystals, too much in the way of "vendors". It'd be nice if it had less magmarians, more crystals with interesting ways to be caught, and if it didn't destroy your equipment.
-Atlantis: That card that won't stop playing villains cards.
* Playing a lot, reading guides and trying out the alternates.