I think it's pretty much a consensus that season 2 doesn't live up to season 1's quality, and even when judged by itself. It is ridden with plots that developed too slowly, new characters that are badly developed and/or uninteresting, and the storyline for virus written unevenly and in the end, rather anti-climatic.
First of all, Hiro's stay at feudal Japan took way too long. They could've developed Tanzei/Adam's character in just a few episodes, because it removed Hiro from the current events and it was just a way to have Ando do something (why would Hiro returns after Ando read his notes from the sword, anyway? Hiro can choose when to return and he could've saved himself many papers). If it was to build up Adam's decension to villainy, then they should've done more for his character then just having him kill a few of the original 12 and trying to release the virus (with aid from Peter).
Nikki/Micah/Monica storyline was very poorly-conceived and developed. Nikki ended up crying and confused most of the time, and became nothing like her character in season 1. Monica is okay, but she is quite removed from the main storyline (even with Bob's involvement), and that iPod didn't really teach her to be anyone extraordinary. Micah is just a wonderkid. The thing is, you can removed these three and not affect the major plot in any way.
Maya/Alejandro/Sylar...need I to say more? At least Sylar finally got his powers back, which doesn't justify all those episodes of him traveling from Mexico with the Wonderless Twins, imho. I hope Maya will grow a brain from now on.
Matt/Molly/Mohinder...it's My Two Dads, basically. Matt has suddenly became much more powerful, while Suresh became stupid and dumb. What will be interesting in Volume 3 is that Matt will probably become anti-company, while Mohinder will be a Company Man. Who will get her custody?
Peter/Nathan...Peter is too powerful, but still doesn't know how to use his powers and make dumb mistakes. Nathan was very underused, and if he does died, I'll be pissed. Instead of creating new, bored characters like Alejandro, they could've given more screen to Nathan.
Besically, season 2 just feel slow and uneven early on, and later they tried to resolve all the plots later, which rushed them and gave us rather unsatisfactory conclusions. I hope season 3 (or Volume 3) will learn its lesson and go back to the quality of season 1.