IMO, I don't know if I'm blinded by nostalgia, or it's really a matter of quality, but I found the Mata-Nui storyline (2001-2003) to be most appealing overall. I loved the Mask of Light movie most out of all the three movies, YES, THERE ARE ONLY THREE!!!
As for the Bohrok-Kal, I loved them also, perhaps more than the Rahkshi, because you just can't go wrong with "talking" Bohrok. Those dudes mean serious business. Another reason the Bohrok storyline is probably my favorite is because it was massively expanded with a flurry of web-animations which added an extreme amount of increased appeal to the story-arc.
EDIT:
Quote: Also, Mata Nui Online game is one of the best games I played in my childhood. The craftsmanship is something to be admired.
1, 2, or both? I loved 2 for expanding upon the gameplay more than 1, but it was buggy as hell.