Although 2D games are alot of fun to play, 3D are my favorite. Better graphics such as in the Metroid Prime series are just better than the original Metroid for the most part in my opinion; although again, the 2D games have so much classicness and can never die...this generation proves that. Super Mario Bros. is probably a favorite of many, young and old.
Personally, I consider the original Legend of Zelda to be 3D. Maybe not true 3D perspective and the graphics are obviously sub par to todays standards by a long shot, but the technology was definitely there and being able to wonder around the world at such an early stage of gaming was pretty amazing back in those days.
2D is better for some types of games, fighters and sidescrollers (Duh.). I'll even say 2D RPGs are better than 3D (The highly detailed monster sprites especially.)
Overall though, I think 3D is just undoubtedly the best thing to happen to games. Games like Zelda are just more fun and complex when you're Hookshoting onto whirling platform. Plus, racing games pre-3d looked just awful. And remember how the original doom looked? *shudder*
As for pokemon/zelda: I wouldn't consider them 3d. They're Top-Down RPGs and they use two dimensional sprites.