>>43517599Mewtwo was cool because he was the epitome of what Pokemon intended to be at the time. A fantasy world being overtaken by clunky sci-fi technology.
All the other legendary Pokemon had myths and legends attached to them. All Pokemon with a mystery attached to them were all super-natural in effect (except with the possibility of Electrode/Voltorb, but that's a gray area.) The only other definitive example of futuristic Pokemon was Porygon, and he was super hyped-up in game about being the first entirely artificial Pokemon, which was just another example in-game of technology overtaking/living with fantasy.
Mewtwo, in-game, used the myths and legends behind Mew to fuel a project about mixing these magical powers with futuristic technology to create a perfect hybrid of power. He was the final cultivation of the themes behind the first games while also not explicitly stating this fact. They explained his creation, sure, but not the themes stemming from it.
Outside of an overabundance of legendaries, I feel like that's another reason a lot of them feel hollow. We're just told 'They're legendary' and that's it or that their role in the story is just there to move the plot along, and if it has a theme attached to it, it's spilled out exactly what it's all about and that's it's only defining trait.