Many people would say that the Bohrok Era was a relatively down time in Bionicle history, what with the advent of direct cloning and all. Really, though, it was an excellent story arc which combined excellent set design with masterful storytelling.
First, let's talk about the set design. Most people would argue that this year should little creativity, what with the blatant cloning in the canister sets. However, I don't think you could say that the Bohrok design was bad. The design was stocky, compact, and with an easily workable gimmick feature. The cloning, personally, was not that much of a problem in this arc. The only time it became a problem was in the next arc, the Kal. Cloning within a generation of sets means that a design is well-built, cloning across generations shows a lack of creativity. Also, we forget the Boxor, the Exo-Toa, and the Bahrag, all of which so great creativity and use of technic beams and smaller pieces.
Now, I'll move on to the best part of the Bohrok Era, the storytelling. And one part of the storytelling in particular: the webisodes.
These were amazing. The way the story unfolded around Jaller, Takua, and co. was so well-written. The creation of the Boxor, the subsequent use of them against bohrok in Le-Koro, so many things were told so well. The Wall-E esque dialogue-less conversations worked very well, and the Bohrok seemed like an impossible threat for the matoran.
also, TOHUNGA TOHUNGA JALA TOHUNGA MAKU HUKI TOHUNGA