I was team Jess.
I'll admit that he was a tit boyfriend. I feel like he didn't know how to deal with emotions and actually be there for someone - he definitely needed therapy or something to work through his crappy childhood/upbringing (not saying thats an excuse though). However, I think he grew a lot - he was the one who got Rory to go back to Yale and wake up, and he wrote a book and paved a path for himself despite not doing well in school. Its just a shame that by the time he was ready and mature enough to be a good boyfriend, that she picked Logan over him.
Saying that, I don't think Rory really deserved Jess in the end...I feel like the revival set it up for him to be her 'Luke' and step up in that sense, but he could've done better. Rory hadn't matured at all in the revival and was kind of awful.