I have personally always have had trouble dealing with 2-D Bosses. It's always about finding their weakspot, I seem to have trouble with it. However, 3-D Bosses are much easier to defeat, as their weakspots are always shown and shown with a high degree of attention.
Puzzle-wise, I think it is about the same difficulty. The 2-D ones use that element to have bird-view puzzle that can be challenging and easy at the same time. The 3-D games really utilize the 3-D to their advantage, forcing the player to look up, down, left and right. Here it's pretty equal.
Overall, I voted for the 2-D games. The 2-D games do a great job of throwing you into an environment and forcing you to understand it, without help. 3-D games are not as good at this, usually having a helper there to 'help' you. This is a factor in why 2-D games are harder than 3-D games.