They really need to give these games more content. As much as I loved GSC, they were fairly short, and compared to every other generation, the levels of opponents' Pokémon are significantly higher. This is probably because they tried to put too much in, with Kanto and whatnot.
This is what I'd like to see:
-Gym Leaders with higher-level Pokémon.
-Beefing up Pryce's Pokémon so that they are higher than Jasmine's. Go ahead and keep Jasmine's Steelix at level 36, just make Pryce's team tougher. If we can beat Jasmine, we should be able to beat a tougher Gym Leader.
-An Elite Four upgrade, obviously, and make it possible to have a "round two" with them. The most logical way this would happen would be to beat Kanto and then come back to the Elite Four, all beefed up.
-Make the Kanto Gym Leaders harder than the Elite Four! If we can re-battle the Elite Four, this would make perfect sense. Come on, a level 39 Venomoth?
-Make the Kanto Gyms themselves more challenging. For instance, make it so that you still have to play Lt. Surge's trash puzzle, and put more trainers in them.
-Rematches with the Gym Leaders. A system like Platinum's seems the most logical choice. I'd like to see this with the Kanto ones, as well.
-Have the Safari Zone open.
-Have the Lavender Town Radio Tower open.
-Have Cerulean Cave (Unknown Dungeon) open. This would be the only way for us to get Mewtwo in this generation.
-The plot needs to be explained more. Even though Silver is Giovanni's son in the manga, this needs to be elaborated on more in the games. And more details with other characters, please. Like Misty! I would love to have something like the Fame Checker.
-The Berserk Gene would come back as a hold item.
-Access to the Sevii Islands. I would hope to have a final showdown with Team Rocket at their wearhouse! I would imagine this would be great for the story line, as well.
-Access to the Battle Frontier. I don't see why we just couldn't take a boat to that location. No change necessary.
-GSC move tutors, with moves like Curse and Zap Cannon.
-Movepool updates for Pokémon. Things that come to mind are Flare Blitz Flareon and Entei, Power Whip Victreebel (even Tentacruel comes to mind), Volt Tackle Luxray and Electivire, along with many other Electric-types, Power Gem Espeon, Persian, Tentacruel, etc.