I don't want to see the 'catch them to complete the dex' return again. It is better when you just have to see them.
I don't want there to be any Hoenn or Sinnoh Pokemon in the grass of Kanto and Johto. The Hoenn and Sinnoh Pokemon can be in the Safari Zone, or in a new place. I don't even want there to be Kanto Pokemon in Johto Grass or Johto Pokemon in Kanto Grass, with the exception of any roaming legendaries like Raikou and Entei. It'll be fun to chase them down through many regions together!
I don't want to see 'wait until the National Dex to evolve into newer evolutions' method return, ever. It's illogical and pointless.
I don't want there to be too less of a story about Suicune, Raikou, Entei, Lugia, Ho-oh, and specially Unown - all of them. There were too little to do with the legends of the legendaries.
I don't want to see Professor Oak in the introduction. He got his one game to introduce. Professor Elm deserves to introduce this one.
I don't want to see normal Pokemon flee from battle, except for in the Safari Zone, if they ever actually existed in the first place.
I don't want to see the shrunk, cut down, and saving space issues to return again.
I don't want to see the Safari Zone, Cerulean Cave, Seafoam Island cave, or the Pewter museum being closed for space saving issues anymore.
I don't want to see a shrunk and cut down version of Victory Road, Viridian Forest, Mt. Moon, or any such be shrunk down anymore.
I don't want to see Larvitar, Houndour, or any such Pokemon to be not found in Johto itself.
Cinnabar Island may be partially destroyed still, but Blaine's gym and the Mansion must remain.
The Power Plant should be functional as it was made in G/S/C, but it should have an area which is still not fixed, for some Pokemon catching, and Magneton and Nosepass evolving.
The Pokemon Tower needs to remain as the Pokemon Tower. There should be a separate Radio Tower.