I think having one left wouldn't be too bad, but I feel like if you had some of them per room with a set movement pattern and had those ones respawn so it can become a little puzzle of working out the timing to avoid them once the randomly moving ones are gone
Hey, I just got to the mega evolution den and it is not a fun area. It's full of pointless fights that give no exp and you can't run from, but they also respawn whenever you leave the room. I honestly feel it would be fine if the fights didn't respawn, but as it is now, it just makes the puzzles...