Yea man, Metroid is survival horror. Sure, it's not Resident Evil but the concepts are all still there. You're on a solo mission in deep space and encountering unforeseen elements, all accompanied by very ominous and dark themed music. I'm not on anything, man, i've played Metroid games isnce I was 8 years old, and there are definitely dark for a Nintendo game. I mean you said it yourself, the dude killed her parents when she was little, that's just dark in general.
And you really can't count Bowser, he's part of Nintendo's history in General. And if you put him in the category of Boss, he is always 'the' boss, same with Ganon (For the most part) Ganondorf on the other hand is part of some intricate plot in Zelda. He holds a piece of the triforce, same with Zelda. The thing about plots with these games is that you are comparing one plot that is graspable vs one that isn't. In almost every Zelda game it is mentioned that Ganondorf has either been sealed in time or has some role in the game, and they also state that he has some tie with the Triforce in some manner. In the Mario games it's always Bowser that's gonna get this ***** peach again. Your ultimate goal? Face them in the climax of the game and beat them. Same can be said for Ridley, but unfortunately he seems to be just another enemy that you'll face among the other bosses you will face through out the game. Hell you don't see Kraid in every Metroid game. If Ridley was such a big deal why is he never a final boss? He should be since this vendetta with Samus is so important.
I wouldn't count Zero mission, it's just a remake of the Original Metroid.