A good plotline for a Peabody and Sherman movie would be for them to travel in time but accidently wind up in the wrong date.
One thing I've wondered is how do they get back? They don't take the Wabac machine with them. It's possible that Peabody has time settings that instantly bring them back to the future, but then again it seems like they sometimes sleep over in the times they travel to (Robinson Cruesoe), and there's one episode where Sherman had to travel alone due to Mr. Peabody being sick, and kept coming back to ask Mr. Peabody for advice.
Regarding the R&B movie, it would have been cool if they'd have at least got more characters from the show to appear in the animated portions. Maybe cameos by Mr. Peabody and Sherman, Dudley Do-Right, and the fairy from Fractured Fairy Tales. Maybe even have Snidely Whiplash help Boris, Natasha, and Fearless Leader. A cameo by Dudley or Snidley would have been a funny way to get them to point out that they'd already been in a movie (Boris and Natasha could have also made that kind of comment, but the Boris and Natasha movie is quite obscure, while the Dudley Do-Right movie had come out a year before the Bullwinkle movie).