The reason Gyarados isn't a Dragon type, for what I've heard, was because Gamefreak originally thought it'd be too much of an overpowered Pokemon if it got a Dragon type added onto it, so they replaced it with a Flying type for whatever reason.
As for the Pokemon I think should've had another typing, definitely Lugia. In the movies it had the title "Guardian of the Sea", it was found in the games inside of an underwater cave, over a waterfall, ontop of water, so why in the world wasn't it a Water type. I understand it'd probably be hard to choose between typings, but Psychic is definitely the less noticeable, so why not Water instead of that, when it's basically being seen like it's a Water type. This is why triple typings would be awesome.