Yes, but not exactly - 2D is still far superior a medium for certain games -
1. 2d Fighters such as the recent Capcom and SNK games are far superior in design, learning curve, subtlety and intricacy than their 3D counterparts
2. 2d Platformers / shooters are still far more intricate and innovative than 3d ones - Eg Sonic Advance, Metal Slug X, Mario World... the only really decent 3d "platform" games I ever played were Mario 64 & Sunshine and these are more 3d adventure games, as is Tombraider. Other games such as Ratchet and Clank, Crash Bandicoot (specifically 2), Daxter etc are fun, but ultimately very simple and basic, if you discount the graphics.
3. Top down or side on space shooters - Never played a decent 3d equivalent, unless you count the Starfox games, and they aren't really comparable examples.
4. Puzzle games in the Tetris, Puyo, Bust-a-move Mould. NEVER played a 3d game like this worth its salt - Tetrisphere is a good case in point.
However, many traditionally 2d genres were massively improved by the advent of 3d, such as exploration / adventure games, RPGs (to a point), and especially Sports and Racing games. Obviously the FPS genre wouldn't have existed before at least plain-3d was invented with Wolfenstein or, to more effective use - Doom
Plus the new 3d versions of RTS games like Warcraft and Ageof are really cool, if slightly unnecessary