We were on the Disney Magic last week. Shrek 2 was on one of the in room channels, so we watched it in pieces all week long. Then they had The Incredibles premEar at midnight on Thursday night, plus we watched it with the kids on Friday. So both of them are pretty fresh in my mind.
I'd say that Shrek 2 was more consistently entertaining. The Incredibles had a really slow start. It spent a lot of time showing how boring Mr. Incredible's life had become, and I thought that section was, well, boring. He had an annoying boss who spent a lot of time yelling at him, and sure enough, that part was annoying. I thought it pulled itself together for the last half, though.
Both are really clever and worth seeing, but Shrek wins in my book.