Super Metroid has a ghost ship that's 8,000,000 times more spooky than anything SOTN musters up. :p There are lots of moments of horror in that game (bosses Spore Spawn, Crocomire, Kraid).
I dunno, SM is oozing with horror atmosphere right from the get-go. I'm not really sure how you're not seeing it, instead equating it to some "guns and aliens" thing or something. It tells me you weren't really paying attention and didn't give the game any chance at all.
Nah it's just my tastes again. SM is probably scarier than SOTN sure, because it's more serious,
almost oppressively so from what I saw.
I usually enjoy spooky, ocassionally goofy fun over hardline horror. Take
Alien and
The Bride of Frankenstein, one of these is obviously scarier than the other inspite of a somewhat futuristic science fiction setting, and they're both really good movies. But I'll always favor the latter because it's in many ways a goofy fantasy that appeals more to my personal tastes. I like science fiction to, but it's not quite as close to my heart. And again I didn't play any Metroids until I was an adult, I'll never have the same tie with that series like I do with Castlevania.
The gameplay seemed more refined in SOTN. I seem to recall not caring much for how Samus controlled compared to the CV metroidvania protagonists, but it's been several years since I tried it. I freely admit I didn't play it for very long so I can't speak accurately in comparison to their level design. Also aside from the gameplay Konami was able to make the environments and characters much more detailed with the power of the PSX than could be done on the SNES, to say nothing of one of the greatest soundtracks in gaming. But even if you're right and SM is every bit as good as SOTN, I'll still prefer SOTN.
Like I previously mentioned
"De gustibus non est disputandum."