No, I'm talking about the actual final boss of MGS3. The part you're talking about is like considering the stuff that comes after BFA to be the final boss of FFX!
Nier's final boss is pretty great, too.
Mario games go from one extreme to the other with this. When they hit, they really hit, but when they miss, they really miss.
Hits:
Super Mario World
Super Mario 64
Super Mario Galaxy
PAPER MARIO (Man, I love this fight so much, didn't think a fight with Bowser could be so epic)
Yoshi's Island
Bowser's Inside Story
Super Mario RPG
Heck, most of the Mario RPGs have really good final boss fights
Misses:
Super Mario Bros. 3
Super Mario Sunshine - Worst final boss ever
--
"Stay with me until the end. Please."
"Not until the end. Always."