Hard to rank them. But...
1. Rannoch Reaper Sequence - it was a cutscene they turned into gameplay, although the gameplay has nothing to do with the gameplay in the rest of the trilogy. It is like an extended one off minigame (laser) proceeded by a turret sequence with a single invincible enemy. Rule of Cool gone amok.
2. Priority: Earth - I'm just going to lump the whole final act of ME3 together. Has a bunch of irritating things, and isn't particularly fun to me. Hades Cannon starts with a shuttle portion where it is hard to move and you can get shot before you can do much of anything. Then there is massive screenshake. No Man's Land is the same old little Reaper units on an ugly map. Missile Battery isn't completely terrible, but then you have the Beam and Citadel portion where you can walk extremely slowly. Compared with Suicide Mission and Illos / Citadel from the first too games, this endgame portion was poor.
3. MSV Estevanico - This is the only thing from ME2 that really rates for me, and that is partly because of the "float" glitch. Seems like nearly half the times I play this mission, it would happen and I would have to reload. And reloading a mission where you just have to walk and there is 0 combat is annoying.
Stuff that didn't quite make it in for me were Firewalker / Overlord Hammerhead stuff because combat is largely optional. On Artifact Collection, you might be able to do it without killing anything on the island at the second, but definitely you can skip all the enemies at artifact 1 and 5.
Won't put the Mako on here either since I have driven it enough and take relatively efficient paths on the side missions.
Husk rush or one million sniper side missions on ME1 aren't as grievous as the top three. They at least involve core gameplay.
Likewise, Saren's Assassins starting from Level 1 on Insanity are pretty hard with some classes, and if you beat that you have nearly got past the hardest part of the game since at this point you can't hardly have any decent talents. Therum Battlemaster is hard if you don't have Battlemaster neutralizing abilities, but this occurs late enough (even at plot world 1) that you can definitely have them.