I think it's the most interesting Poke-minigame yet, and I actually voluntarily play it. It's a puzzle-y sort of thing, while at the same time being similar to traditional battles, just with interesting twists. I hate it when my poke gets confused and attacks itself until I run out of time, though.
(Please not that I never played Heartgold/Soulsilver and so have not played Pokéathlon. Please don't hate me)
"I desire to go to Hell and not to Heaven. In the former I shall enjoy the company of popes, kings and princes..." - Niccolo Machiavelli