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Sounds good. Maybe not his grandfather giving him the Latias but his grandfather and grandson capturing it together. Grandfather would do more work. Like the story, a lot. Keep it simple and just have Hoenn with a few extra places, I would.
I think you should concentrate on quality not quantity. I'm not dissing you but checking out some of your sprites, a lot of them are clearly rushed. And there are too many fusions.
Good luck, all the same.