I personally believe less is more. Unless it make sinces with the story or the lore behind it. For example, the island guardians in Sun/Moon. So I agree that havinv 7-8, even 9 legendaries are perfect. I just dislike if a legendary is plugged in for the sake of numbers. However, I like the way how ORAS & USUM, does it though.
And yes writing a story with the established legendaries can be hard, but not impossible. Just flesh out their own lore some more. Here's one in mind, celebii is seeking help because something happened to dialga and time is being disrupted. Or shadow lugia defeated kyogre and is now turned into a shadow pokemon, and now manaphy is missing. So prince phione came to your help to stop lugia and kyogre and save manaphy. Idk something like that.