Because they are kid games they just have really basic plots. The audience, parents, etc have come to expect a certain story. While its not great, in don't really play for the plot or story, at all. I actually kind of enjoy making fun of the nonsensical stuff.
I will say though, plot wise, I liked gen I best. Not for the story so much as the hundreds and hundreds of interpretations of that story by fans. Its been pulled apart, dissected, looked at, heck we even got a special mini series on the games. There is just so much to look at, plus its the most familar to me as I've played those games the most. Gen 2 will always be a favourite of mine, they were just such great sequels and took Pokemon in an awesome direction with the breeding mechanics, etc.
I wouldn't mind, in the future, meeting a villan who didn't care about destroying anything, but just cared about like collecting Pokemon. Like, they literally want to catch them all so badly they don't just want one of every Pokemon, but actually try and steal every single pokemon alive... Part of the plot would have like, an empty safari zone you have to fix and maybe even the final gym could be missing their team because it got stolen and you have to rescue their Pokemon to get your badge. It would be a poke fan gone horribly wrong. It would be really simple, believable motivation. You could call them the collector or something. I think that's part of the problem with Pokemon plots... They just make them so complicated they become outlandish and laughable. Team Magma and team Aqua had such complicated motivations and reasonings for more land and sea, it just became really ridiculous. Fortunatly, these remakes are making their motivations and plot more reasonable and believeable.
Gen 1 and Gen 2 had bad guys being bad guys more or less. They started to try and change it from there and it got weird. I mean X/Y to me was the worst villans to wrap my head around. They want the world to stay beautiful, so they'll destroy it before it gets ugly?!? Like WAY too complicated... We want a more beautiful world. Do we start a recycling program or destroy everything??? BETTER DESTROY EVERYTHING. They made it seem like a team that was just after money in the previews. That would have been so much more believable. I know they want to tie in the legendaries, but their has to be a better way than that.
But this is all sort of off topic. I'm not really crushed that the plots are weird and dumb. Like I said, I kind of enjoy laughing at them. And I'll enjoy Hoenn because of the slightly ridiculous plot.