zelda had the best transition of the 3 and metroid i think had the worst one.
mario had a good one but it lost its pro platform feeling other that mario had a good one
i cannot comment too much on metroid but i saw some videos and it look way too different. on the gcn games it looks more like another mission then we go home. the nes version felt like let's kick some @#%.
zelda in some cases made it feel more epic and gave it that feeling of I am link but i have no right to argue with the snes/nes zelda OG players.

Super Mario 64 is STILL at or near the top of it's genre almost 20 years later, it's aged incredibly well unlike Ocarina of time.

I don't get it. You criticize Zelda for losing nonlinearity and criticize Mario for losing linearity. Are you saying Zelda games should be nonlinear and Mario games should be linear? Also, the Galaxy games are quite linear. 

I don't know....I find the control scheme in Mario 64 to be worse than that of OoT. It just seems like the way Mario moves is very wonky in that game compared to the way Link moves in OoT. At least for me anyway. 

Mario is still near the top of its genre , but OOT is still widely considered the greatest game of all time.

That's exactly what I'm saying. The fact that you think Galaxy is linear just highlights the issue. Galaxy isn't even remotely linear in level design when compared to literally any 2D Mario.

When Zelda and Mario were first created, they were created to be opposites. Zelda was mean to be non-linear and completely open, favoring combat and free exploration. Mario was ment to be tight and linear, favoring platforming and level design.

Now the 3D versions of each have err'ed towards the center of that spectrum, which is what Metroid was made to fill, as opposed to staying on stark opposite sides.

Yep. The franchise that kickstarted the platforming genre should lose it's tight platforming focus.

Reading some of these makes me sad.

That's a really great question. All three games are among the best ever made.

In terms of influence, I think Super Mario's move to 3D was the most successful. It led the great migration from 2D sprites to 3D polygons, and it influenced generations of 3D worlds. Ocarina, which built upon the foundation of Super Mario 64, was most successful in terms of overall game design. And Metroid Prime was most successful in terms of difficulty. In 2001-2002, there weren't many fans who thought Metroid would make a seamless transition from third-person 2D to first-person 3D. It remains, to this day, one of Nintendo's most impressive (and unlikely) achievements.

Hmm, tough choice.

I played the original Super Mario Bros. and The Legend of Zelda on VC before trying out Super Mario 64 and Ocarina of Time, and based off my enjoyment of those games, I'm gonna have to say Zelda.

(I haven't played enough of the Prime games to have a solid opinion on Metroid's transition.)

Zelda, though I really miss the old school 2D Zelda (at least I had 3D Dot Games Heroes).

2D Mario is far more superior to me than 3D.