I was thinking about past games, and it seems that the player is periodically encountered by the Champion throughout the main story.
In addition to the Champion, this generation I'd like to see the box Legendary Pokémon encounter the protagonist as well.
I imagine that some people are thinking of the player figure looking up at a floating Rayquaza on Route ### and thinking either "That'd be awesome!" or "Whut? (.—.) "
I think it would be a nice change for the box Legendary to resemble Greek gods in the way that the Legendary deities can change their God-form to a humanoid form and interact with people.
The Legendary form is what appears in the distance, far enough to keep the main character from seeing any resemblance of the Pokémon form and the human form. The evil team has been trying to track down the Legendary, but the human form keeps its Pokémon form elusive. The evil team uses their tech to find the Legendary but are confounded by detecting "false positives" whenever the human form is around.
Only when the evil team figures it out and captures the human form does the Legendary reveal itself to the player.
This is much like the human that Latias disguised herself as in one of the anime movies.
This!!!!!! Or even if it doesn't have an accessible "human-like" form, just being able to disguise itself like Latias does would be an awesome plot device. We know that Zoroark can mimick people, like the backpacker - so why not give a legendary a similar ability? That would be the best!