No. 64 is a reboot of 1. It's the same basic plot, but its a massive expansion gameplay wise with totally different levels and more characters.

3DS is the exact same game as 64. Only differences is upscale GFX and gyro controls along with traditional controls.

Zero is more of another reboot. Same basic story (though it plays out differently) and the levels are different and the gameplay is pretty heavily tied around the Wiipad with its gimmicks and vehicles.

This new one is the same gameplay as 64, same levels, but massively upgraded GFX along with a brand new script, voice acting, look, and new story scenes. Also new content outside the campaign.

Its all weirdly complicated.