You've got to remember that when deciding which pokemon is better, seeing how they'd fare against each other isn't always the best way. Shedinja can pretty much always beat Kyogre one on one, but to say shedinja is better then kyogre because of this would be foolish.
I used to think Dragonite was the strongest pokemon, but then I got an arrow to the knee. Oh Arceus, I am saying this and I never even played Skyrim.
But with all seriousness, I did. I remember when playing R/B/Y and G/S/C, Dragonite always seemed so powerful under Lance's care. With the hyper beam mechanics back then and me using mostly fire/water/grass typed pokemon, it was a true challenge.