2011/2012 are most definitely my favorite years of Hero Factory. 2011 introduced the beloved CCBS System, and tried a lot of new builds and techniques with it. In addition, it gave us Witch Doctor.
The following year, 2012, gave us Breakout, and Breakout gave us lots of improvements to 2011, such as better coverage, more build variety, and new pieces that would still be used today. In addition, it had lots of sets, including our first titan hero, and the first vehicle in two years!
The weakest years for me would have to be 2010/2013. 2010 was really LEGO's worst year for constraction, and it shows. Other than the nice titans, 2010 was just the Inika Build and Av-Matoran Build, but it was even worse, adding in those useless Ben 10 parts, and some new molds that would never be used again. And the limbs were probably no better, maybe worse.
2013 had some great versions of the heroes, IMO, but the villains dragged down the whole year. After two years of exciting villain builds, we get some half-complete humanoid monstrosities. Along with that, Rocka and Bulk were very lacking, and though I like the "titan" sets, they aren't the most impressive when compared to other years. I don't know, it just felt like the designers weren't trying very hard with this year of sets.