The story that became filled with utter useless fluff that only served to make it seem larger and more complex than it really was. Also, the hand a lot of fans had in this outcome while the story was being written.
Very little female characters existed, the ones that did were mediocre at best. Symptom of putting aside one village of six to be "the female village" and only having one of each element represented in each set wave (creating a massive disparity in male and female characters). Roodaka was an utter joke that didn't belong.
The massive shifts the atmosphere kept taking. You start on tribal, mysterious Mata-Nui. You then suddenly shift to a big city, an advanced society, with all kinds of technology and political corruption. You then shift into the post apocalyptic with more political backstabbing and genetic mutations abound. Then the story becomes darker, edgier, gritter as characters are killed more often and more violently, as sets are made with bloodstains on their faces, as you have every individual conspiring against one another and begin creating sad spinoffs of eldritch gods. You now have war criminals whose only characteristics are "violent, evil and dangerous."
Makuta. Makuta was a dark shadow they could slap on anything to make it seem "intimidating" or to make disjointed storytelling act as if it was all planned that way because the great villain had plans within plans and could apparently predict the future and plan for every loss, even the surprising losses. The character lacked substance, lacked personality and was about as interesting as the nearest box.They also named him Teridax.
I'll never like the Mistika as sets. I'll never like most of the Inika as sets. I disliked a lot of later Bionicle designs, I disliked the overuse of silver, I disliked the change from brown to orange, I disliked how the heads and masks kept changing, making them less and less compatible with the earlier masks and collectibles, I disliked how large and lanky the sets became and how out of proportion they were. On the bright side, I enjoyed the Voya-Nui Matoran.
The gender restrictions were frivolous and stupid.
Those are most of my cons with the G1 line.