I remember playing through GS like cake, and then hitting the Wall named Will. Whitney excluded, all of the gyms were pretty easy, and its not like the Rockets were ever much of a threat. But then I would finally get to the E4 and my Pokemon had barely broken 40, and Will's Xatu double team was too fast and too hard hitting for me to get past, at least without heavy casualties. I'm not saying lighten up on the E4, I'm saying ramp up the rest of the game. Gens III and IV both had my Pokemon crossing the Lv. 50 threshold by the time i got to the E4, without having to grind. I want the same in HG/SS.
Also, I want to see the Gym leader's team go nuclear after the National Dex. It was cool to fight the Kanto leaders with Johto Pokemon in the originals, and I imagine it would be just as fun to see the Johto AND Kanto leaders beef up their teams with the entire 4th-gen roster after I get the National Dex. I want to see Faulkner with a Starraptor, and Brock with a Rhyperior.