The books in the year 2006 were among my least favorite. At many points felt like the characters were rushing from one battle or crisis to another without pause, and the characterization in these books (in my opinion) was very weak. Subsequently, Prisoners of the Pit ended up being one of my favorite BIONICLE books because it got to explore the Toa Mahri, their relationships with one another, and how becoming Toa had affected them much better than the 2006 story had done for the Toa Inika.
What changed for the BIONICLE storyline in 2007? The biggest change was the introduction of BIONICLEstory.com and the first story serials. And I think that while their own quality may be contested, they helped to relieve some of the bloating that the main story had undergone in 2006. Instead of the main story having to make room for minor characters from the sets like Umbra and Irnakk or combi models like Protodax, Botar, and the Kardas Dragon, the story serials could deal with these kind of characters (as seen in Dreams of Destruction, which focused on the store-exclusive characters Lesovikk, Karzahni, Sarda, and Idris, or Brothers in Arms, which focused on the store-exclusive characters Mazeka and Vultraz). Instead of the main story having to keep tabs on fan-favorite characters from previous story arcs like the Toa Nuva, Roodaka, the Rahaga/Toa Hagah, the Order of Mata Nui, and the Dark Hunters, the story serials could keep tabs on their adventures (as seen in the Toa Nuva Blog, Federation of Fear, Destiny War, Dark Mirror, and Dwellers in Darkness).
These things freed up the main story as told in the books to focus on the characters who actually mattered most: the current Toa team, their current allies, and their current enemies. The books could spend more time on characterization and world-building. They didn't have to do so much jumping around between spatial and temporal settings. They didn't have to have so many characters who got in the way of the Toa just because there was a set or combi model to promote and the designers didn't give a lot of thought into how to fit those characters or situations into the main storyline.
I can't tell you for sure whether the serials are every bit as bad as people remember them. I just skimmed through the 2007 ones to remember what they were about specifically, and the writing is weak compared to the books — in some cases, weaker than I had remembered. The fact that my memories of the later serials were not fond enough to even go back and skim them is telling. Perhaps part of the reason the serials got more tangled and bloated as they went on is because, with more and more characters being introduced to the story and fewer and fewer books to fit them in, they started to suffer the very same fate they were meant to save the main story from. In any case, I definitely don't think that the serials are themselves redeemed by the purpose they served, but perhaps I still owe them some thanks for what they were: a pressure release valve of sorts to reduce the out-of-control expansion the main story was losing the ability to deal with on its own.