Tough choice between Mario 64 and OoT

I think OoT tops it though

I picked Metroid. Metroid Prime somehow had the exact same feel as Super Metroid. I don't know how they did it, but it is amazing. I think it was all the attention that was paid to the environments.

For Mario and Zelda, I think the 2D and 3D versions of those games each has its own distinct feel and play style. There are differences between them. They are still great, but they do feel like their own franchise.

All 3 did great transitions, but Zelda was the best one. I consider every 3D Zelda better than any other 2D ones (except for ALttP, which I consider to be better than SS).

The majority of forum-goers are against 2D Mario fans. Sales, luckily, say otherwise. 

...not quite sure how Prime "isn't Metroid."

The essence of Metroid is isolated exploration of a non-linear environment while slowly becoming more powerful through personal discovery. Metroid Prime is...isolated exploration of a non-linear environment, and you slowly become more powerful by discovering various powerups and upgrades. I suppose you can argue that Samus controls differently, but it's very much in the same vein as the 2D Metroid games.

On topic, I'd say Prime was the best, followed by OoT, and then SM64. Personally, I think Prime has held up much better over time than either SM64 or OoT, and no one has really been able to actually improve significantly on Prime, while OoT and SM64 have been outdone on several occasions.

In terms of influence; Mario. In terms of sheer quality and enjoyment on a personal level; impossible to decide, it's a tie for me.

There are four core values on which Metroid was created: Action, Exploration, linearity, and platforming. In no particular order, but of equal importance. Not non-linearity, masked linearity. It was meant to take the action and freedom found in Zelda and mix it with the platforming and linear progression found in Mario, creating an experience that is inbetween the two.

The progression through Metroid is extremely linear. There is a "right way" to go. What creates that sense of freedom is the fact that, although there is usually just one path forward, you are never explicitely told what that path is or how to proceed through it. It was never about non-linear progression, but about exploration.

Prime gets the action, exploration, and the linearity down, but almost entirely drops the platforming. Because platforming is such a huge part of the way Metroid is designed, this changed a lot in the switch to 3D. It completely changed the level design to something extremely horisontal (like Mario) when Metroid prided itself on is verticle level design. The shift in perspective had a detremental impact on the types of power ups she recieved, with less of them focusing on platforming and more focusing on a new visual "scanning" gimmick (not using gimmick in a derogerory way). That was never what Metroid was about. Also, the power ups where never merely about "getting more powerful." They were about getting more platforming abilities. Almost every power-up in the 2D games is a platforming power up.

Prime is only Metroid in genre to me. It happens to be a game in the franchise that falls into the "metroidvania" subgenre, but that's the extent of it. It lacks the level design and platforming focus that Metroids 1, 2, and 3 had. If it wasn't part of the franchise, it would be unrecognisable. Can't say the same for something like Super.

For the record, I think Prime is much better than Mario 64 or OoT as well, but I don't think that means that it transitioned to 3D the best.

Metroid had by far the best transition from 2D to 3D, atleast for me. Mario 64 had it's flaws ( Mainly due to releasing so early when compared to the others ) and Zelda released on hardware which didn't do it justice in my opinion.

Mario, this was back in as early as 94 when Mario 64 was first unveiled, it's not easy to do a 3D platformer and it certainly wasn't easy during the jump from 2d to 3d for gaming in general. Both Zelda and Metroid owe a lot to Mario 64 themselves.

The one that has a metacritic of 99.

Credit to all 3 though, especially metroid for really having to reinvent the gameplay