Nothing beyond Red, Blue and Yellow are legit Pokémon games to me. Sure they added in some awesome new Pokémon and new moves but the story is virtually the same every time.
More over they watered down "Legendary Pokémon" with so much garbage they can hardly be called legendary anymore. I mean seriously there were the 3 elemental birds, Mew and Mewtwo in Red, Blue and Yellow. That was it. End of story. They are legendary because they are so rare as to be unheard of. So powerful that they melt the inferior eyes of the unworthy if such a person manages to see them. That made them legendary, now though they might as well be common Pokémon because of how many there are.
To get to the birds you had to explore a few caves, for Mewtwo you had to do a bit more, but not much. They were unique to an individual player, but not to players as a whole, as most everyone found and caught them, and they were certainly not overpowered in any way besides Mewtwo. Compare this to the Regi-trio in the third gen, where you had to find a very out of the way underwater cave, translate a series of messages from braille while trying to learn braille, then complete a long sequence of events just to unlock them, after which point they could be sent to the next set of games to unlock a final one, and you have some seriously well hidden Pokemon. It was hard to find these guys without help, really hard. Discounting Gen 5, I'd say legendaries have become both more powerful and often more difficult to get. And they can't just not add more, that would break a fundamental part of the game. I'd agree that they add too many each time (except with X and Y so far, just 3 new ones) but I wouldn't say that makes them any less worthwhile.
The story of the original games was also very light and only served to set the stage and act as a backdrop to the gameplay. The others have evolved some while staying to the same structure, but Pokemon isn't a heavily story driven game, it's about what you bring to it.