I personally felt that a lot of the atmosphere was lost after '06/'07.
The Golden Years aren't called the Golden Years because they had good sets, it's mostly because it's when Bionicle had the greatest atmosphere; every corner of the story was shrouded in mystery. Who are these robot things? Why do they have powers? Who or what is the Makuta? Why do they live on the island? Why is the island important?
You could say that the atmosphere became less potent because there were less questions to be answered as the story went on, but I think Bionicle actually maintained that important aspect of mystery and intrigue all the way up to '07. '08 got extremely sci-fi and less fantastical, but I think that's down to the aesthetics and plot (as cool as the Codrex is, I personally think all of '08 could stand to maintain a similar atmosphere to '01-'03).
'09 was a step in the right direction. It brought back the mystery with a new planet entirely, but it never got to explore that planet. We never knew Bara Magna as well as we did Mata-Nui, which to me is a shame because the original map of Bara Magna had a lot of potentially interesting places that just never held any actual importance.