>>53019409The first two games had a creepy mysterious undertone to them that the later games lost as the world became more colorful and fleshed-out. In RBGY and GSC, frequent references to real-world animals, the references to real-world locations and events (like the Space Shuttle Colombia exhibit or how SIiph Co. has a branch somewhere in the middle of nowhere in Russia), the underlying space theme, and the fact that people seem to know so little about them all imply that Pokemon are invaders from another world that only appeared relatively recently; they're dangerous, unknown variables that have worked their way into the otherwise natural ecosystem, and it gives a sense of urgency to the fact that the brightest minds in the world are scrambling to learn and catalog as much about them as possible, making your job catching them and recording them have an actual meaning. The presence of ancient ruins (that never really get explained), the fossil Pokemon, and the legends of Ho-Oh, Lugia, Celebi and the Three Beasts in GSC further expand the mystery, because they suggest Pokemon have been around a bit longer than people first realized.
...Then the later games dump all of that and go with the whole 'Pokemon have been around for forever and have always been the equivalent of real-world animals (which no longer exist in canon), but we somehow still know nothing about them even though they were here all along' thing that they've been doing ever since Shudo died. There's no more mystery about them or their origins, since they're considered perfectly natural these days. There was some promise with the Ultra Beasts, which basically took up the role all Pokemon had in Gens 1 and 2 as 'dangerous unknowns from god-knows-where', but they dropped the ball with them completely.
