Ah yes, the classic controversy among Bionicle fans. Hero Factory fans don't really care because their theme wasn't replaced. (Until it was.)
I'm going to cover this methodically, because that's how I do things.
My Exposure/How it Began
In my early LEGO years, I pretty much had whatever stuff my parents bought me. They later signed me up for the LEGO Club Magazine, which was when I became fully aware of LEGO's range of products. My first issue included the last comic from the Karda Nui era, with later issues including Bara Magna comics. I read them once and put them aside. Bionicle was always That Robot Theme With The Weird Names for me. When Hero Factory came around, it was easy for me to understand because I was there from the beginning. I really got into it and followed the story, but I never collected many sets. Fast forward to 2015, and I was ready to dive into Bionicle Gen. 2. However, I don't really have much nostalgia for either theme.
Now that I've gotten through that, which may prove important for this article, I can give my thoughts on the stories behind the themes.
Bionicle has a really deep and expansive story, which I really appreciate. Unfortunately, the only part of it I experienced firsthand was the Bara Magna saga, which I consider to be one of Bionicle's low points, which ended in a cheap sellout. *Cough*Stars*Cough. A downside of this complexity is that it is hard to follow unless you've been there from the beginning.
Hero Factory also could have had a good story, but instead it blazed a path that Ninjago and Chima followed: sacrificing story for getting out as many waves of sets as possible. I enjoyed the Rise of the Rookies and Ordeal of Fire, but it went downhill after that. I did enjoy the novels, though.
Bionicle has a diverse range of heroes and villains that make for an interesting universe. The standards are not always conformed to (Tuyet) and there's just a lot of development and many trials that people face. (I'm looking at you, Tryna)
Hero Factory has some interesting characters that had well-described personalities at first, but they were just empty drones in the show and comics. They faced no trials other than seeing how many opponents they could blast. The only ones who received any hint of personality were the villains. such as Meltdown and Speeda Demon.
Bionicle has received a lot of sets over the years. They started out very simple and were kind of ugly, but this simplicity also had a certain charm to it. Later figures had better articulation and cooler designs. It was the kind of development you'd expect from a new toyline, kind of similar to what Transformers went through. Bionicle also had a lot of collectibles that were cool (Kanohi) and lame sometimes (Kanoka).
Hero Factory's sets are really what redeem it in my eyes. While there is no good story or personality in the franchise, the figures are superb. The 1.0 figures had limitations, but that Surge is still a personal favorite of mine. The 1.0 villain designs are also some of the best of the franchise, with figures like Thunder and Vapor bringing a lot to the table. The CCBS system is also an important factor in constraction that led to the return of Bionicle. While I really like most of these figures, I despise Brain Attack and Invasion From Below. FOR SOME REASON THEY THOUGHT THE NAMES HAD TO BE IN ALL CAPS and the Hero designs lost all traces of uniqueness. The villains had original designs, but were just plain ugly.
I sounded really harsh towards Hero Factory, but I really like it besides the lack of story. I also sounded like I really, REALLY favor Bionicle, which is not true. I do prefer it over Hero Factory, but only because I enjoy a good story with my toys.
I hope you will see that I have written an honest, fair article that has not been written while wearing any nostalgia goggles. Bionicle is the winner for me, but both franchises have their ups and downs. I don't understand the hate directed at Hero Factory, and I'm sure had they been branded Bionicle figures there would have been no complaints.