I found out about Samus from Super Smash Bros. erroneously reffering to her as "he". If I had been a little older and had seen the release of Super Metroid, I might have been able to appreciate her presence, or at least get her gender right (after so many years of calling her the wrong pronoun, I still struggle with the proper one).
Nintendo has managed to succesfully transition Mario and Zelda accross platforms through the years, but the same can't be said for Metroid. The series has all but fallen out of prominence, despite the well-received Metroid Prime, and it may have somethign to do with Metroid's conspicuous absence on the Nintendo 64.
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Nintendo did a tremendous job of featuring its biggest stars on the Nintendo 64. Mario, Yoshi, Kirby, Donkey Kong, Link, and even Pikachu all got at least one game of their own for the system. Pikachu even got a special version of the Nintendo 64. There is someone missing from that list, however. Someone who also needed to be featured and was sadly left out. That someone is Samus Aran, of Metroid fame.
Imagine what she could have done on the N64 and how that could have given Retro Studios even more to work with for Metroid Prime and given them a head start on making 3D Metroid titles. Additionally, by skipping an entire generation of consoles, Nintendo lost out on the opportunity to further develop the Samus character and the story of the Metroid series.
Not only did they lose an opportunity to explore the character, but the series lost its momentum. By the time Prime came out, a whole new group of gamers, who had been exposed to new version of Mario and all sorts of other games, had no familiarity with the series.
Samus was never really part of my consciousness. I was six when Super Metroid came out and 14 when Metroid Prime came out. That is a huge gap, enough to make me totally oblivious of old titles and lacking in anticipation for the later ones. Metroid Prime might as well have been new IP. It wasn’t until college that I finally played Super Metroid, but it seemed more of a relic than a part of a living series.
Just before the release of Metroid Prime, Shigeru Miyamoto spoke about the hiatus during an interview with IGN.
I know that the American people have been eagerly anticipating a new Metroid game. I have been asked about it many times! Even through the entire Nintendo 64 period we were thinking of ways to produce a new Metroid title. We couldn't come up with any concrete ideas or vehicle at that time.
If Nintendo really couldn't come up with a good enough idea for an N64 release, it's a good thing that they didn't force anything, but the proposition is somewhat difficult to believe. Whatever the reason, Metroid was absent for a huge window of time and a whole generation of gamers were unable to really internalize the Samus. This is not to say that a series requires an annual release or anything so drastic, but if developers want longevity and relevance of their series, they may want to make sure they at least get a game out on each console generation.