Well, the fact that Pixar has had to produce films at a faster rate after the merger has certainly affected production. Before the merger, apparently, everyone in the company worked (in some capacity) on every film. Now, due to the accelerated release schedule demanded by Disney, that's not possible.
The merger era has also seen far more sequels than were developed in the pre-merger era.
I haven't seen any of their films since Up
, so I can't really comment on their recent output's quality, but reviewers have certainly noticed a decline.