I don't want any changes to the plot or Johto gameplay.
I don't want to see the early NPC levels skyrocket. I know the Elite Four was kinda weak, but keep in mind, after facing them you had EIGHT MORE FREAKING GYM LEADERS to fight, if all of the Elite Four have level 60 Pokemon that only leaves a a twenty level inclination from Lt. Surge to Red, the equivilent of fighting Brock with his level 14 Pokemon and your rival in the Elite Four with level 35 Pokemon. It should be evenly spaced out.
I don't want the return of Johto Poke Balls.
I don't want the apricots to be cut. Think about it, the special Poke Balls from D/P/Pt could be not available in stores and only available through the old method.
I don't want Typhlosion/Feraligatr/Maganium following you around without choosing to. It's one thing to have a cute little Chikorita trot alongside you through Violet City, it's quite another to walk into Pallet Town with a Feraligatr backing you up.
I don't want to see 3rd and 4th gen Pokemon running around Johto. Maybe in Kanto after you get a National Dex, but I want to GET a National Dex, not start with it.
I don't want to see exclusion of now basic items added since Gold and Silver, like gear shifting bikes, VS Seeker, ect.
I don't want to see stupid (and I don't mean bad stupid, I mean low IQ stupid) berries like PSNCUREBERRY or PRZCUREBERRY when we now have the better berry equivilents.
I don't want a shift in the Gold and Silver HMs, I don't want the Whirl Islands to lack whirlpools just because Whirlpool isn't an HM.
I don't want the Red Gyarados to be treated like a normal shiney in wifi (it should have it's own seperate search, like a totally different Pokemon), but with the Pikachu colored Pichu, it's starting to look like there might be a seperate kind of alternate color Pokemon for the like of them.
Finally, I don't want the English version of the game to be called "Heart Gold", it really doesn't roll of the tongue easy. FIRE Red, LEAF Green, and SOUL Silver are okay because they end on soft sounds (er, fuh, and ll) while Heart Gold on the other hand sounds wierd because of the strong consenents following each other. Maybe GoldenHeart and SilverSoul versions would be better.