Looker on the S.S. Anne would be fantastic
That girl that wanted the Pokémon with the flower design? Have her mention or have a Munna, and say something about dreams coming true
I want them to go more into the daily lives of some of the gym leaders:
See Brock at Mt. Moon searching for fossils, perhaps he is in charge of the Pewter Museum.
Misty could have another date scene like in gen 2, but I'd rather something new. Maybe she can kick off the Cerulean Cave post game sidequest, and/or at some point maybe see her swimming for some competition or something
Lt. Surge could be involved in the Power Plant quest, and in getting Zapdos
Erika could be part of the raid on the Team Rocket Game Corner
See more about Koga and the Safari Zone, maybe have Janine in it too and show their relationship, and him training her to be a gym leader or something
Sabrina and the Dojo master's rivalry. Maybe they can put their differences aside to aid the player in Silph Co., Maybe talk about her being an actress
It would be amazing to involve Blaine way more in the plot regarding Mew and Mewtwo, and maybe even Moltres and the Sevii Islands
More Giovanni stuff would be all right, don't know what else though. Maybe make it possible to view the scene where he and Silver part ways from HGSS
Lorelei can help you get Articuno, plus the Sevii Island stuff
Not sure about Bruno, maybe he could also be a part of the Saffron City Psychic vs. Fighting type gym, maybe Bruno used to be the gym leader of Saffron City?
Agatha can go into her rivalry with Prof. Oak. Maybe have a scene in Pallet Town where she shows up. It'd be awesome if it turns out she's also from Pallet Town!
Lance could talk more about Johto, although I'd love it if he were involved in a Mew or Mewtwo sidequest. One can dream
Just some thoughts, haha