OOT. There is no equal.

Super Mario 3D World took what was a mediocre 3D Mario (3D Land) imo and made it way better, not only visually but also with the multiple playable characters, so I'm gonna go with that. Super Mario Galaxy 2 was also great but it was just more of the same tbh, which isn't a bad thing at all, just didn't impact me as much as going from 3D Land to 3D World did.

What exactly qualifies as a sequel here? Is it as broad as any game in a series besides the first? Or does it have to be a direct followup to a previous game, like Phantom Hourglass?

Regardless, I'd say Super Metroid. Virtually universally regarded as one of the best games ever, and with good reason.

The way I will take this how:
- I played 2 or more games in the series

I would say maybe from AC Wild World ----> AC Lets go to the City -----> AC New Leaf! New leaf just had most of the things I wanted in the game:
- More customization of the world and your house
- More things to do

Super Mario World 2: Yoshis' Island

Hard to decide! Super Metroid, Mario World, Majora's Mask... I can name quite a bit. But I think the one I keep coming back to is Metroid Prime, which just so happens to be my fave game ever. I guess just like Mario 64 and Ocarina of Time, it was a 2D franchise that transitioned beautifully to 3D.

A true sequel should improve and build upon its predecessor, but I feel Prime did so much more than that, considering how much of a transition going from 2D sidescroller to first-person action-adventure was.

I second this. So far, the only thing that came close was Breath of the Wild, but Ocarina of Time still has the edge for me because it had more personality/remarkable moments.

Mario Kart 8 Deluxe. A great sequel to my favorite Mario Kart.

Maybe something from this:

-Mario Galaxy>Mario Sunshine
-ALTTP>Zelda2
-Mario64>SuperMarioWorld
-Pikmin3>Pikmin2
-Mario Kart 8>Mario Kart Wii
-Yoshi's Woolly World>previous Yoshi game