I'd go out of my way and say that I think most of the missions are so damn hard because they are designed -too well-. Yes, I think the missions are incredibly well designed, but that's the problem with them. It's kinda like the Evil Overlord List, Everything is so well done that you as a player can rarely outsmart the enemy. You find a hole in the maze? Too bad, there are terror drones behind the tree you can't see nor destroy. Things like that. In a way, the best design is to have flaws in the levels, "non-designed" flaws the variety of player may or may not able to notice and use it to their advantage.
As for my votes, I think most of them are self evident, with the exception of Peace Treaty, which everyone seems to like, but me. It's the mission I got stuck on 'till I decided to just go through the missions using cheats. But it's not really the difficulty why I think it's bad, It's the lack of tactical logic. You have a base there, dear Soviets, why the hell you don't build the Beacon there?? You're saying that the stadium is the best location for it (even though it's only a few meters from the base)? Then build the base around the stadium!