Hard to say, pokemon are weak and strong to certain types making some better than others, if you consider this then you know water is the most common type and fire is a huge favorite.
For that reason I believe a Kyogre with thunderbolt is technacally the strongest, but that said many things can beat it, such as a Groudon with Solar beam, I think in order to be the strongest pokemon you gotta be the best all purpose pokemon, you gotta be able to learn moves like Assist and Metronome, probably have a good ability to save you in battle and have decent stats, I supose if your willing to evolve your Skitty you could have Delcatty which might be strongest, there is also Togekiss which can learn both of said skills.
If they ever come out with a Ground/Ghost type with Assist, and Metronome, that'll be the strongest pokemon ever.