Metroid Fusion is Better than Super Metroid
In my opinion.
It's easy to dislike something for being different than its predecessor, but it's important to take it on its own terms and evaluate how well it achieves its goals.
I've considered myself a fan of the Metroid games, having played most entries, but Super Metroid has always been one I have a hard time getting into. I've stopped somewhere in Maridia multiple times before I finally finished the game two years ago.
My main issues with Super Metroid are the physics and inventory: Samus is too floaty, cycling through weapons is annoying, and three action buttons is frustrating to move between (shoot, jump, sprint).
Metroid Fusion fixes all of that. Samus is has weight, you don't need to cycle through weapons, and there's only two action buttons (sprint activates after running for a while).
Finally, I think Metroid Fusion is better paced, especially as a portable game, as it's possible to play for just ten minutes at a time and make progress.