1. Mario
2. Zelda
3. Metroid
4. Final Fantasy

Worst is poor Sonic:(

GTA followed by probably Final Fantasy. I don't think any of the other games truly maintain the gameplay fundamentals birthed in their 2D predecessors. All though many of those games are masterpieces in their own rights, they are failures in that regard.

Mario. Super Mario 3D land is awesome! And Zelda too. ALBW is also awesome!

Castlevania 64, Contra for the PS1 and Sonic Adventure.

Super Paper Mario did it in one game. Lol.
Metroid, easily.

I would go with Zelda

Mario, platformers as a genre had a nightmare transitioning into 3D, SM64 was pretty much the template for 3D gaming on how to build 3D worlds, Zelda's jump to 3D is actually heavily based on SM64.

everything you listed there, the rest is just the matter off preference.

If I had to pick just one, and absolutely just one. I think it is Metal Gear Solid. You know why, because unlike a lot of franchise mentioned I would say both 2D and the 3D was great. However Metal Gear to Metal Gear Solid, it was an alright franchise, that became one of the greatest game of all time. 

GTA, all the way. All the other franchises had to make serious accommodations to fit into a 3D realm, but GTA only got more complex (and fun). GTA bloomed in 3D, whereas all the other choices were already pretty amazing in 2D.