I had a Sony Xperia Z1 Compact before my Fairphone 2, and I didn’t notice any disadvantages yet (I got it for 8 months now). The main function of the modularity is to repair broken parts, but as far as I know there are some rumors that threre might be a better camera in the future. Speaking of the camera, you can see some pictures taken with the Fairphone 2 in the gallery (here: FP2 - Pictures Gallery)
EDIT: I forgot to mention that I never had any major issues except one, which was my own fault. And thanks to the Forum, I was able to solve it very quickly 