When I first played it, the boulder puzzle in Seafoam Island gave me the most trouble. I remember having to ask my brother's friend for help getting past that part.
Rock Tunnel was pretty hard without Flash, but still manageable with memorization, patience, and careful attention to graphics and sound.
Nowadays, the only part that really bothers me the the size of Mt. Moon. At least Rock Tunnel was narrow and linear, while the other dungeons had unique variations. Mt. Moon, on the other hand, had so much empty space, I'd have to fend off many wild Pokemon just to get from one wall to the other.