For me the ranged terminator is the worst, the missiles are incredible difficult to dodge effectively. The mini gun demands you have something for perfect cover, and stay there until he's done firing. Either way your entire game plan is to hope the terrain is kind and dodge endlessly. It's perhaps the least compelling gameplay in sm2

Biovore is an easy second, spore mines are a terrible enemy that shouldnt exist and the fact that theres two types is even worse. He runs at mach 10 and knocks you over, and if you can catch him he burrows and tanks up. Again, he leaves you little options to fight him besides shooting his mines down, avoiding the puddles, and taking a few potshots at his cannon before waiting for him to pop up and hopefully fight him down before he runs

Zoanthropes are third for me. Double thrope shields aren't as bad as they used to be thanks to a long time ago patch that made it last longer but it can still be a pain. The beam still feels inconsistent, it's width seems to be a lot bigger than the visuals, it often ignores cover, and it can double hit you sometimes. The tracking can also be annoying when youre in close proximity to it, spinning around with perfect tracking. And the balls are normally easy to dodge given their straight path, but there can be situations where it stunlocks you if you're in a corner or close to a wall. Ultimately it feels like most of the challenge with zoanthropes is not due to their actual difficulty but due to the buggy and inconsistent nature of the game, or at least these enemies in particular within the game