I think that they should also emphasize a bit on the sub-plot of the Red Gyarados.
I hope, but doubt, that HG/SS will have some Shiny Gold references too, such as Carlos (although maybe a different name) or Lance, after clearing out Team Rocket from Mahogany Town, he will give you a Pokémon. I don't know about a Clamperl, and the Dex may start out as the Johto Dex, but that would be cool in my mind.
Carlos, as I said before, would also be a great addition to the game because of the challenge. Something along those lines to throw some extra "kick" into it.
And I like the idea of more Manga references, besides just Red. There should be a sub-plot around that. There, actually, should be a whole sub-plot built around characters such as Blue, Red ect. See, in Gold and Silver, Blue was the Viridian City gym leader in place of Giavonni who is out of the picture in the game.
They should build a whole separate plot into Kanto. At the end of the game or sometime in the middle of the Kanto adventures, you should find Giavonni (wherever he is off to).
I think tossing in a whole other region, ergo Hoenn, is too much. The levels would be way to high for a video game. It would be fun, but it would be too much. I mean you could train and all, but the game couldn't hold 24 gyms. Maybe the Orange Islands would be good, because its only 4 gyms. But the Sevii Islands, Orange Islands, any kind of extra thing is hard to put in the game because it already has to regions. (Note: If they remove Kanto from the game the amount of people who are going to buy it will probably drop by 75%) In fact, I would buy it, but I would only buy one, and I wouldn't trade my Pokémon over to one of the two as I planned.
They should definitely update the PokéGear. I still like the idea of PokéGear, but it should have more of a Pokétch aspect to it. Maybe it will be a Pokétch. But it shouldn't, really. It should be more, bigger, better. An update PokéGear could possibly include Pokétch features, the original PokéGear features, and maybe PokéNav features thrown into one PokéGear!! That would be really cool!!
Okay, I'm done rambling. xD