For all five generations, the overall gameplay has remained pretty much the same. You're a beginning trainer, you receive your first Pokémon and set off on a journey to fill the Pokédex, challenge all eight Gyms, and eventually become the new region Champion. That's all stayed the same.
I mean, of course things have changed from generation to generation. That's inevitable; I personally would find each generation more boring than the last if it was just the same stuff each time. That's what I like about Pokémon, it manages to stay fresh with each game that comes out.
In terms of Pokémon design, I don't see what's wrong with having Pokémon that "don't make sense," as you put it, インフェルノの津波. I think it would be pretty boring to have the same animal-based designs over and over again. :/ I personally like that they're branching out and doing some different (even kind of ridiculous) kinds of designs, they're getting creative.
So has Pokémon strayed from its roots? No, I don't think it has. It's still the same "gotta catch 'em all" gameplay that it was when we were kids. The Pokémon may be different, but the game's still more or less the same.