Lava damaging your Pokemon instead of you, with a configurable chance of burning & damage calculations sorted by types/abilities weak, resistant, or immune to fire
Fall damage likewise also damaging your Pokemon, with flying types/levitate/maybe some mons also resisting/are immune to fall damage (could calculate via Ground type maybe)
Poison clouds having a configurable chance to poison/toxic your Pokemon.
All outside of battle, of course.
And so-on and so forth. If you REALLY wanna get crazy about it, Splash/Lingering Potions have a lot of effects.
The big reason why I suggested this is because I thought of how, theoretically, one could add Atum 2 support for Pixelmon spawning with all its traps and whatnot in an interesting way, and this popped up. This could also affect things like gyms and certain "challenge" structures where there's new conditions the player has to work around.