I honestly liked Fusion the least in the series (Hunters doesn’t even qualify). Fusion had annoying dialogue, annoying save/nav/ammo points, and annoying retraverse limits. Other M was at least pretty and would have been a master piece if Itagaki hadn’t been fired from team ninja.
i don’t remember how to embed video but there’s a link to YouTube. My favorite memories of Metroid are when I realized Samus was more powerful than the singular items I found her. The coolest is the recharge embryo. 
Not cheats and not singular items, not even told you could do them. These powers came from friends and magazines. Fun surprises like this are what I love.
Similarly, (o.g. Metroid) I fondly recall the save code “Justin Bailey” that dressed Samus in a purple bathing suit and green hair. Because if you died at the end, you might not be able to refill your tanks. Therefore this code saved many of asses — and it looked cool.
Last but not least, I just really liked the 3D play ground and sound in Metroid Prime. The water on your visor, the reflection of your face in an explosion of light. I don’t like either of primes control schemes, but everything else is a dream come true.
