+Metroid Prime
- Ocarina of Time

I've got to admit, I like OoT (3D) more than Prime, but Prime lay the foundation for Prime 2, my favorite game of all time. Prime 1 is my least favorite of the Trilogy.

People only think the first is the best because they played it first. Same with OoT actually. At least that's my opinion on it.

Story? Prime 2 is a lot better (this includes scan logs).

Graphics? Prime 2 looks a lot better. Sanctuary Fortress still looks gorgeous today.

Bosses? This one is easy, Prime 2 is far superior in this regard.

Level design? Prime 1 had a lot of annoying platforming sections which don't work well in first person view. The Phazon Mines were just annoying imo. Prime 2 streamlined this.

I guess some people can't get over the difficulty of Prime 2 which is ok, it's not a game for everyone. Although it really isn't a hard game. Never unfair in the slightest.

+Metroid Prime
-OoT

I tried to rally both sides against Galaxy but alas, twas not to be.

sup.
prime is long been dead.
i've been busy the entire day.
i'm sorry.
please understand.

+ Galaxy
- OoT

+Galaxy
-Ocarina of Time

+ Galaxy
- OoT

+ Super Mario Galaxy
- Ocarina of Time

+ Super Mario  Galaxy

-Ocarina of Time

This is it! Either of the games deserve to win

And now we head towards the ending we've all seen coming for a while. Oh well. The top 3 being Mario, Metroid, and Zelda is fitting though.