There is now a total of 50 legendary Pokemon. Removing the event only ones we are left with 35. They aren't going to have solid reasonings for all these creatures being shoehorned into one game, nor do they need to. It's better to just accept it at this point.
They were doing a fine job of it in Gen 4 and 5, so it's not a matter of "there's too much," it's a matter of "do they care enough to implement reasons for it." Evidently, they didn't this go-around, and that's all there is to it.