One is having the Legendary Birds be a side quest in Kanto. I'm thinking of creating new areas/temples or towers where the Trio are worshiped and people in the past were able to summon them. However due to a past feud between the trio and their followers the temples were destroyed and the means to summon them were lost. Until Team Rocket rediscovered the means and use it to capture them.
Another idea is using lures to attract Pokemon from other regions that have migrated to Kanto. Like Unova lure or Alolan lure.