First off, there was kind of a huge disappointment not so much regarding the movie as it is that it actually didn't have the Rocky and Bullwinkle short at the beginning. Instead it had something about aliens constantly trying to find another planet to live on because every one they picked blew up or something. Steve Martin was the voice of the Alien leader. It was a fun cartoon, but not the Bullwinkle short they reported. I hope it comes to DVD, is paired with HTTYD2 or at least gets released online.
As for the film, without spoiling too much, they did change a few things for dramatic effect to fit in a movie's story structure. But surprisingly not much. Sherman is more like a child, Peabody's relationship is much more of a parent then a reverse pet owner. They referenced the heck out of the first episode but changed Sherman to an abandoned baby and the WABAC machine is both an actual time machine (not the what if machine he converted it into) and it's far more technical (again, dramatic effect). But Peabody does still make awful puns after every adventure (during some even)... it lampshades it too.
There are a couple jokes I have to say were unfortunate choices (there's one that's a pretty nasty accidental double entandre). A couple unfortunate dated references... but nothing really detracting from the movie... or as bad as the villain falling into a pile of elephant crap like in George of the Jungle. But overall, the best Jay Ward cartoon based film there ever was, and not nearly as insulting as the New George of the Jungle cartoon. In terms of Jay Ward movies, I liked it a lot more than both GOTJ films (my favorite until now), but in terms of Dreamworks' films I liked it much better than The Croods (which I really enjoyed quite a bit), but not quite as much as Kung Fu Pandas 1+2 (my favorite). Probably as much as I liked Monsters VS Aliens. Which is quite a bit.
OH! And while they did credit Jay Ward for producing the series, they also credited the real creator, Ted Key.