This is what you do... You 1.) Hack Pokemon Colosseum to allow the game to read and play a first or second generation game, then, 2.) Hack the console itself to allow the cartridge plug-in first used for Pokemon Stadium 1 and 2 to be plugged into the Gamecube in some way
This allows you to use Pokemon Colosseum game as a midway point to separately read and exchange information of the two cartridges
Second method: Get a Gameboy and Gameboy Advance link cable. Then, strip the wiring. Mod and hack the thing until it acts as an override that allows trading between the two generations... Basically, you're trading your first or second gen Pokemon to the link cartridge itself, which then converts the Pokemon data to information the third gen game can read, which then transfers over to the third gen game
NOTE: This method may require the two cartridges to be hacked so they don't trip out when they're hooked up.
Third method: Hack your Nintendo 64 or Gameboy to allow for Wi-Fi connection. Plug in your RBY or GSC and "trade" your Pokemon, via Wi-Fi, to your Wii or directly to your DS. Whichever is more capable.
And there you have it!