The Pokethlon looks a lot more entertaining then contests to me.
I just hope that a Pokemon's Pokethlon stat limits aren't determined in a way that prevents certain species from having a fair chance at winning some of the events.
That's a part of the strategy, though. You need to build a team of "Pokethletes" that can easily cover all of the five stat areas, to make a well-rounded team. In Contests, any Pokemon could be "smart" or "cute" or "beautiful"--which didn't make sense for Pokemon that weren't smart-looking (Slowpoke) or cute (Nosepass) or beautiful (Quagsire).
Would it make sense for Slowpoke to be able to beat every other Pokemon in the Dash Hurdle game?
All in all, while the two are very different, I like Pokethlon more. Contests are fun, and I hope they're built on in future generations to make them better time-wasters, but for now, the Pokethlon is my favorite side-quest.