The GameCube hosted three distinct Pokémon experiences. Your "best" depends entirely on what you want.
Both Colosseum/XD link with GBA games (Ruby/Sapphire/Emerald/FireRed/LeafGreen) via GBA-GCN cable for:
If you can only play one, hunt down XD. It's the most complete, polished, and replayable Pokémon experience on GameCube.