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I'm gonna say SA-X. A lot of games do the whole "You aren't strong enough to fight him yet" thing to convince your character to beef-up a little, but Fusion was probably the first game to prove those words without a generic "supposed to lose" RPG battle.
"Not all who wander are lost." http://whitetigershiro.blogspot.com/
There are some good parts in metroid 2 where you can't see the metroid, then there's the sudden "boss encounter" that makes you just jump out of you skin, as the boss pops out of nowhere, especially when its a highly evolved metroid.
SA-X, when you first see her and it zooms into her face. Ridley X as how it Suddenly Appears and screech's or roars or what ever it was at you. Umm The Chozo spirits when first encountered. The metroids in Echoes when they break the the barrier or glass or what ever it is when you least expect it.
I'm not really a game freak but i do play games alot lol
I'm gonna say SA-X, it was the only boss in the series that was actually "scary" because you go threw the almost whole game not being able to kill it. Anytime I saw it, I was scared of being seen, and really scared when it was chasing you because you know if your not fast enough, your gonna die.
I'm actually surprised that nobody said Quadraxis, that would be second on my list. You fight them stupid little machines that are kind of a pain to destroy, then you see a huge one and think, "how the heck am I supposed to destroy that?".