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One thing to keep in mind is 2D's main advantage over 3D is that it is much much easier to tell distance. This is main problem with 3-D platformers.

Mario - 3-D: 2D Mario's gameplay is defined by power-ups and momentum based jumping (and of course brilliant level design and pacing). Galaxy showed that power-ups could work just as well in 3D. Momentum is fun thing to master, but it really doesn't bring that much more to the game. On a whole, Mario games are also retreating from being about making clutch series of jumps so the main advantage of 2D really isn't that strong. On the otherhand 3-D allows for greatly superior exploration (M64), and can make for just as riveting linear sequences (SMG).

Zelda-3D: I'd say the core of zelda is puzzles and using items. Both of these elements really benefit from being 3DD. Overhead view in contrast to 2D really has no significant advantages over 3D.

Metroid-2D: Metroid was about power-up based exploration. Although the Prime series is quite excellent, its never quite captured this gameplay with the same subtlety as its 2D counterparts. In contrast to Super Metroid (essentially the pinanacle though Zero Mission does a great job of reusing its elements) Prime's use of the power-ups is extremely heavy-handed; most all of its physical navigation is extremely limited in comparison to 2D Metroid. Even the one power-up it implements superiorly to 2D metroid (The spiderball from Metroid 2 for the GBA) confines you to very obvious, predetermined tracks. I think Metroid may one day be best in 3D, but until it can properly implement the vast array of Super Metroid's power-ups I'll always think of 2D as providing the superior Metroid experience (I'm waiting for my speed booster, shinespark, and single-wall wall jumping in Prime =D)