I rewatched all the movies in 2009. I thought the shift from TUC to GEN was the most jarring. It really shows that the movie was written by people who were out of their element in this installment.
I thought Data's emotion chip was annoying too. And, really, is that the best time and place to install an emotion chip? Data has always had a hard time grasping humor, it's nothing new, so why should he feel his growth has reached an impasse any more than it has before? Another consideration is that with never having had emotions before -- with the exception of "Descent" -- what would Data's level of emotion maturity be? Even the youngest officers have two decades of experience dealing with emotions. What does Data have? He'd need to have psychiatric examinations to re-evaluate if Data has the temperament to function in Starfleet.
There might be more that comes to mind but it'll have to wait until Tuesday.