I personally loved the Hero Factory FM program from 2010. It was hilarious and definitely warmed me up to the theme.
Some sets I have the best memories from are:
William Furno (my first HF set)
Stormer 2.0 (first CCBS set and found at LEGOLAND California in Dec. 2009)
Brain Attack Stormer
Stormer Freeze Machine
Bulk Drill Machine
Personally, I’m glad that BIONICLE and Hero Factory are kept in separate continuities. I like to enjoy both without having to worry about events overlapping.
I do wish we could’ve found out what Christian Faber was going to tell us a few years ago about the original plan of HF and how the story bible was very complex and detailed. IIRC, there was something about how the true protagonist of HF (the theme) wouldn’t be from HF (the organization).