People complain about the plot becoming too deep and they are like "Pokemon is about the Pokemon! The plot takes itself too seriously!" then there are people who were like "There needs to be more involvement with the villains and the plot and it needs to be more deep and philosophical and violent or whatever!"
Well, now with Black and White, the plot is very heavy and it has been getting heavier every generation. It all started with D/P/Pt delivering a very philosophical message regarding evil and suffering and whether a world without such things could truly be a utopia like Cyrus wants and is he really even a villain or a man with legitimate motives regarding ending sin in the world, but taken to the very extreme with a god-complex to boot.
Nor was Team Galactic just a regular street game, but an organized cult with their leader worshiped as a god who could end evil and suffering.
Then Team Plasma takes it to a whole level... I won't try to spoil it for you waiting for it to come in English to play it, but it takes the plot like one would see in an RPG.
Which wait a minute, isn't Pokemon an RPG to begin with? RPGs are known for their plots, right? Then shouldn't Pokemon be worthy of a good storyline like any other RPGs?
But wait, then there are those people who are like "But Pokemon isn't Final Fantasy! I don't want it to become like that! Pokemon is taking the plot too seriously! It's conforming to all of the rest of the RPGs!! That's what made it different!"
Yes, but unlike the other RPGs, it actually takes place in modern times which a majority of RPGs tend to take place in a medieval fantasy setting and there is a lot more team customization as well rather than your four designated heros that you have throughout the journey.
The whole issue as far as plot has always been a split... Seriously, fandoms like to nitpick, that's just what they do. Some more than others. Like I know the some people in the Megaman fandom who are like "If it isn't 8-bit, then it sucks" those people have shallow minds and don't keep their minds opened to say, the Zero or X series and actually play it and clear their eyes of the bias and look at the game by itself.
Which is what I do whenever I play a game, I always look at it by itself before comparing it. Comparisons are rarely good because you never end up equal. The only time comparisons are good is if you are comparing it to an ultimate standard.