TLDR; 2006 is flawed due to marketing but schway due to cool storyline, revolutionary sets, and cool characters.
First off, the marketing in 2006 was stupid. There's very little debate on that front. People that like it most likely enjoy it for the sole purpose of making fun of how awful it was. I know that's why I do. The Piraka Rap was garbage, Free the Band was an atrocity, and the Move Along ad is pretty hilarious in hindsight.
However, there's signficantly more to the year than how it was advertised.
The story was top-notch, and one of my favorites that BIONICLE has offered. High-stakes scenarios that up-the-ante of the overall conflict, interesting incorporation of characters (Turaga, Matoran, Toa Nuva, Legacy of Evil), surprising plot twists (Toa Nuva getting defeated, Inika's creation, etc.), and a plethora of cool characters such as Axonn and Brutaka. The year also built the general BIONICLE world quite a bit, with the introduction of the realm of Karzahni, the Order of Mata Nui, and basically the entirety of Legacy of Evil.
The Piraka were good villains. Completely independent of whether you think the Barraki were better or whatnot, the Piraka fulfilled their roles excellently. They were interesting because while their personalities are (arguably) similar, they were able to portray a wide range of character traits as a unit. They could be fearsome opponents to the Toa, funny when they were bantering with each other, unpredictable due to their backstabbing nature, dark because of their sadism and intentions, and even a little sympathetic when you think of the reality of Zaktan's transformation. They were also a first for BIONICLE in that they were an entire wave of six (seven if counting Vezon) characters that were all distinct characters rather than clone sets. Because of that fact, they are, IMO, more interesting and unique characters than basically any villain from the first 5 years except for maybe Makuta (although I would argue that Makuta's true character depth only came later on in BIONICLE's lifespan; beforehand, he was really just generic black-and-red evil dude #43214324). They were effective villains, when all was said and done, and they did their job pretty well.
I also thoroughly enjoyed seeing the Matoran from the original trilogy return as prominent characters and take up the mantle of Toa. It was a very interesting twist in what could have potentially been just another standard Toa Nuva operation. When I was younger, I just thought it was really cool that we got a whole new team of Toa who were interesting characters that WEREN'T featured in flashbacks (I hated flashbacks, which is why 04 and 05 rank so low in my list of favorites. Mostly 05 though, because of how inconsequential it was. 04 isn't that bad because it legitimately had an impact on the larger storyline). I do somewhat feel that the creation of the Inika somewhat undermined the "You don't have to be a Toa to be a hero" message that was circulating amongst the Matoran and Voyatoran who, by the way, were also awesome characters that added a lot to the year, but if forced to choose I would definitely keep the Inika.
2006 also had a plethora of fun and creative games; I may be wrong in saying this, but I believe it had the most games out of any BIONICLE year? Like, say what you will about VNOG from a game design perspective, but it was certainly a unique and inspired take on the "Online Game" formula, and it's very evident that a lot of work went into its design. It's a heck of a lot better than 2007's garbage games.
From a set design perspective? The year was revolutionary. Universally loved? Definitely not. The shift from function-based construction to more poseable "action figures" was definitely controversial, for very good reason. There's no denying, though, that 2006 was a very innovative year that changed BIONICLE AND general constraction design basically forever, be it for good or bad. I'm in the probable minority that vastly preferred the Inika build to the function-based constructions of 01-05 for sheer poseability factor, although the fragile pieces somewhat killed my enjoyment.
BASICALLY, no, 2006 wasn't perfect. Its marketing was questionable at best, some aspects of it could've been done better, and let's be honest, the artwork for the comics was pretty lackluster. That being said, I think it's an incredibly strong year and while I'm hesitant to say that it's my favorite BIONICLE year... I can't really think of another year that eclipses it in my mind. The only one that would even come close and possibly be better objectively is, admittedly, 2007. I think the Ignition Trilogy is BIONICLE's strongest point in time from a storytelling perspective, which is why both 2007 and 2008 also rank highly in my list.