It's really hard... I'm mostly basing my opinions on the actors. Robert Downey was the only good thing about IM2, but Chris Hemsworth and Tom Hiddleston were the only good things about Thor 2. It's easy for me to say that RDJ outclasses both of them, but the fact that IM2 wasn't a good movie doesn't help. Thor 2 was a great film and both Hemsworth and Hiddleston delivered, but like I said, RDJ just gets to me all the time.
Despite how many feel, I actually enjoyed IM2 a lot, it wasn't perfect but I never felt that it was as bad as many would want to believe. That said, out these two I personally enjoyed Thor more. The pacing was far better, a lot more action and the movie just seemed to flow with the story and never felt to lag to me. All of the characters at some point got a little spotlight as well which I liked. Overall, I thought it was a great movie.