To be completely honest, in my personal experience.
Difficulty didn't rise, simply the annoyance factor of mechanics did..


Instead of throwing 1 shinies at you, it throws 3. It's a cheap way to give a sense of difficulty.. Ends up feeling more like I'm playing a scrolling shooter game than an MMO tbh.. Also, memorization will make everything immensely trivial.
So,
first clear = challenging
second clear = faceroll