It's true that the Kobo app doesn't work in 4.2, but Kobo has put an announcement up in the Google Play store that they are aware of the problem and working on a fix. I wouldn't let this seriously influence my decision one way or the other. The Kobo app will work soon, I'm sure.
On the other hand, Google updated my Nexus 7 to 4.2 yesterday, and has Kobo even announced the 4.1 upgrade yet? Given how much faster my Nexus is with 4.2 over 4.1, I would think the benefits of being a "flagship" device would make the Nexus the clear winner here.