@supergamerfreak: Not to veer too off-topic, but quite the polar opposite was true for Pokémon's beginnings. If you take a look at the pre-history of the franchise when it was only a design concept, Tajiri brought the idea for Pokémon ("Capsule Monsters" at the time) to Nintendo
numerous times before he actually got a deal; Nintendo was in fact so concerned towards the project that they sent Shigeru Miyamoto to collaborate with Tajiri, who eventually became a mentor-figure to Tajiri, which in many ways you could argue did help launch Pokémon to success by 1999 (financially and as an icon because of Miyamoto's idea for the version split for example, as well as Miyamoto providing Pokémon's close affiliation towards Nintendo's older first party IP, namely Mario and Zelda). And even with the "help" Nintendo sent, the
5-year development process of Red and Green was so straining on the original Game Freak team that it almost destroyed the company (at one point Tajiri couldn't afford to pay the development team at all, and had to have his parents fund the project it was that desperate), and at many times throughout the duration of those five years there were inevitably strong decisions to abandon the games entirely, to prevent the crew from quitting their jobs and complete bankruptcy. You could make a Hollywood-caliber drama/story out of it
. Needless to say, it was perseverance that bore Pokémon in the first place (not trying to be sentimental or unfairly patronizing of Game Freak; it was genuinely the case), not any sort of planning on Nintendo's part or the corporate behemoth of a structure we have now, with five generations, countless games and fans, 12+ movies, yada yada (not to say the corporate structure is any worse obviously). The coincidences of later Pokémon in original works was just the result of how Game Freak's own workflow and schedule panned out, in addition to the anime folks representing those Pokémon on-screen after the creation of those Pokémon had gone on under Game Freak in a stage preceding the public eye. Nintendo only would've given business direction and an approval on it, at least until they got more involved after the first generation/season/etc. Nintendo had better things to do in the early '90's, or so they thought, haha.[/history lecture…]
and @ShadowDark: I think it's gonna be interesting how future remakes, assuming there are any, tackle the issue of plot. Moving into the third generation a lot of version differences occur in the realm of storyline, so that'll be another element to incorporate when a developer has to consider new features for the games and how they will be integrated with the original games' content. Albeit, after you beat RSE, the games revert to that more traditional similarity, but I guess we'll have to wait and see what Game Freak or whoever else does with that.