While I have liked and disliked several parts of both the plot and the sets over the years, I think my main beef with G1 came late in its run. Ignoring nostalgia for the first three years, and my dislike of the style in 2004-2005, I feel like the BIONICLE universe went off the rails in the online serials.
As the universe grew, we got more and more characters. I liked their inclusion, but it quickly grew too much when all the unimportant characters from earlier years started having serial roles. Greg even worked with no plans, which led to wild plot turns and a bunch of characters that had no relevance but kept popping up. A lot of plot points and twists appeared, but had a flat conclusion. Some were forgotten outright in favor of a new twist.
The serials were the only story posted online. The good old online games and Flash animations fell into obscurity for newer fans. The story became confusing for anyone who hadn't followed the series since it started. Reading a chapter you might feel inclined to pop open several wiki pages, only to find references to ten other characters and locations you have to read up on first.
This is in part why they chose to reboot the series on Bara Magna in 2010, I believe, but of course we were left with serials from the original universe and a brand new setting which the older fans didn't feel any connection to.