There's definitely been a tone shift. Like others have said, a lot of it has to do with hardware limitations (don't forget that the Game Boy had been out for the better part of a decade when Pokémon was released), but it's also something that happens organically to long runners. First the inconsistencies are addressed, things are retconned, then with the introduction of new characters comes new lore that has to fit in with the original, and so bit by bit, the world gets expanded on, and the series develops (and redevelops) its own identity. Not to mention the influences of its era.
I have no doubt that some changes have been conscious decisions, but a big part of it just sort of happens over time. I would say that Pokémon as a whole leans a bit towards the idealistic side at this point, but it isn't exactly afraid of exploring darker themes, either. The world has gotten a lot more complex compared to the relatively one-note disposition of RBY.
>>33294294>>33295302I'd argue that gen 2 already put that "trend" on the map. A lot of Johto Pokémon have different eyes and are just more colorful in general compared to the majority of the original 151. A great way to tell are some of the evolutions for Kanto Pokémon.
Basically, the variations have been there from the beginning, and if Pokémon was ever going to expand beyond its intended run, it was always going to reflect that. Personally, I say the more variety we have, the better.