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Red, due to being severly underleveled (highest level pokemon was 63, 2nd was 59). But favorite hardest battle would be Green/Blue (not as underleveled by as much...but still really challenging).
The Clair and Lance Double Battle in the Dragon Den. My Feraligatr was only Level 63 when I faced them and that was my highest level. I only managed to win by using a lot of items because my team was really underleveled when I saw Lance's stronger Pokemon.