Personally I'd like them to have the Sevii Islands, Cerulean Cave (Like In FireRed and LeafGreen) also other new areas like the Frontier and A Desert, They should have a special area with the 3 Legendary birds and also Uxie Azelf and Mesprit these would be a brilliant addition I feel and would also enhance the games story, also just like MD Explorers of Time and Darkness they should have several alternate stories for instance like the one with FireRed and LeafGreen they should add the change in Pokemon that the Elite4 have once you have won the Johto League they should introduce more pokemon for instance ones from the Hoenn and Sinnoh Region they should have corresponding Legends from the 3rd and 4th Generations making it more interesting for instance a story with Dialga in SoulSilver and Palkia in HeartGold they're should also be the to catch Darkrai, Shaymin, Arceus and various other legends too whether they're via Wireless Communication or Cheat System also like in DP&Pt they should have the Poketch Application so you can locate the legendary dogs because in the GB/C/A versions I was fustrated at the chances of encountering the Dogs based on the fact that I found no way of locking the on the Map.
I also feel that after these series whether it's straight away or after a possible Crystal Remake they should create the penultimate game I don't mind what the name is but with the 4 generations and also a brand new 5th generation totalling up to 600+ pokemon hopefully on the DS not DSi but with extra features with for instance the ability to take a picture for your trainer card. Also they should have more legendary pokemon and Dozens of different stories for instance new teams (i.e. like Team Rocket, Magma, Aqua, Galactic and Possibly 2 more following the Sequence from (1 TR), (2 M&A), (1 G) & (2 5th Generation).
Have I got good suggestions or what let me know what you think because I'm thinking of contacting Nintendo.