Ok so some notes.
1. Its good that you acknowledged Zygardes unique attribute and trying to think of a way it would work. That's probably one of the challenges chainsaw isn't looking forward towards. I think complete form would basically be when the breed scene happens not a side scene. Pairing Zygarde with admin/scientists was actually what I was thinking also.
2. There is no kalos queen that's anime only so not going to show up most likely
3. Side scenes with mega evolved Pokémon makes sense since this would be the time tho threesomes with the human characters is ehhhh, having the humans lead to solo side scenes makes sense.
4. Pokemon showcase is an anime only thing as well though I do know there is a beauty contest type thing in the game so perhaps something similar could be pulled with that tho who and what that will lead to is up in the air game Serena isnt necessarily the same as anime Serena