I have a couple of ideas for things in the game recently:
1. An idea for a mewtwo side event for kalos. mewtwo has two mega forms, and in xy you can find a mewtwo in pokemon village. What if mc and mewtwo travelled to the cave after hearing that mewtwos mega stones are hidden in the cave, and when they arrive in the cave they are ambushed by a SHINY mewtwo. The story is that this mewtwo was a backup that was made in case mewtwo escaped, but this one also escaped and travelled all the way to kalos. They would probably be far more bitter then mewtwo, because they were made as a backup and therefore would see themselves as inferior to mewtwo. Also, maybe there male or futa? (Team rocket probably would want there bioweapons to reproduce so they could get a full army.)
2. Now this one is a big stretch, but mc's mother had him after being banged by a ditto, right? Pokemon recently announced a new spin off called pokopia, and the main character is a ditto. (you may of seen it, you may of not.) What if the ditto (mc's dad) was later released by its trainer and winded up on a remote island, before creating a small harem/village with the local pokemon. (like father, like son) mc spots the island one day on the boat, and docks there, and the ditto recognises him. (Dittos probably have a 6 sense for knowing who there kids are there's with the amount they have)
Again, these are just ideas, and I know your busy with trying to balance your life and updating the game.