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spemanig said:

All three were unsatisfactory in my entirely not humble opinion. Metroid lost good platforming and vertical level design, Zelda lost nonlinearity and exploration, Mario lost linearity, platforming focus, and started recycling content. None were good transitions for their franchises.

Though not technically a 3D platformer, but an isometric one, it gets closest to the core of the franchise while sticking to a 3D plain, so after almost 30 years, I think the only one to make a 100% real transition is Mario. Followed distantly by Zelda only because of Wind Waker. Followed even more distantly by Metroid because of the obvious Prime.

EDIT: I shocked at how many people think 2D and 3D Metroid are similar. They aren't. Like, not at all. Prime is great, but it isn't Metroid. One of the best games of all time. One of my top 5 games of all time. The best first person game of all time. Not real Metroid. It literally plays nothing like those games aside from the level progression system.

...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.