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The Doom example doesn't exactly refer to first-person shooters as a whole, but rather to a specific reputation the early FPS-es began getting in the early 2000's, exemplified by the Genre Throwback first-person shooters such as Serious Sam, Painkiller or Strafe. Namely, the belief that Doom and its kin basically consisted of walking forward through repetitive environments and casually killing huge hordes of stupid enemies with tons of blood and guts flying around. The example points out that the gameplay in Doom differs quite a lot from, say, that of Serious Sam.
The entire Pokémon example seems to be less "Unbuilt Trope" and more "Early-Installment Weirdness."
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Looking at the UnbuiltTrope.Video Games page I notice a lot of Pokemon entries that don't seem to fit, and Wolfenstein 3D and DOOM (and most 'classic' FPSes still use the mechanics they invented, like scrounging for health. Modern FP Ses also use historical settings frequently, and what tropes are being unbuilt are had to find.
Also this whole thing is kinda inaccurate. " Team Rocket was the first of several villainous "Teams", antagonistic groups that come into conflict with the player over the course of their journeys. Unlike their successors, they are portrayed dead seriously (while most grunts in future games are played largely for laughs), they are not involved with the Legendary Pokémon in any way (though adaptions did make them responsible for Mewtwo), all their operations are criminal in nature (compared to the more cult-like/terrorist organizations that followed them), and, while they are defeated before you can get all 8 badges like most Villainous Teams, their story doesn't end there; the final Gym Leader is their boss, Giovanni. "
I'd say a case could be made for Team Rocket in that their plans never get to start due to the player's interference, unlike later villainous teams who keep on trucking until the player defeats them after the plan's gotten to critical levels.