I like both years, but if I had to choose a favourite, it would be 2007.
Matoro's Sacrifice was one of the more memorable and powerful moments in the overall story (at least for me). I really like how it was portrayed in Downfall, describing in detail what he was thinking about and the thought process that went into saving the other Toa Mahri. I also liked how in the comic, it showed glimpses of his past forms as a Matoran (along with Matoro wearing the mask).
I also liked that 2007 was a year that had less clone-sets I really liked how the Barraki's designs varied based certain real life sea creatures; along with each of the Toa Mahri sporting a unique look, rather than all having the exact same build (to be fair, the minifigs were not that great IMO).
The titans were good. I really liked Hydraxon, with his load of weapons, as well as Maxilos (decent build and for story reasons). Although I thought that Gadunka was questionable IMO.