This movie didn't flop because it was in 2D
I've heard that this was a great movie that was unjustly ignored at the box-office. As someone who likes Pooh but didn't see this movie I can easily see why it would underperform and the animation isn't the problem.
First of all the movie is only 63 minutes. 63. That is extremely short. As good of a movie this may be, parents aren't going to want to spend 11 dollars just to entertain their kids for one hour. Think about it, two parents and 3 kids plus popcorn and soda is about $80 worth of money for one brief hour. In this day in age people want to go to longer movies to make sure they've gotten their moneys worth. Thats why most animated movies now are at least 90 minutes.
Second, Winnie the Pooh stories have almost always been small scale misadventures in the Hundred Acre Wood. Because of that, there really isn't the need (or so people feel) to see this on the big screen. People go to the movies to see spectacles. Immersive ariel shots, epic battles, breathtaking cinematography. Pooh isn't going on some epic quest that needs to be enlarged on a giant screen to be felt. Pooh stories are always more intimate. So while this may make the story more endearing it doesn't make it a must-see event that people need to see in the cinemas. The Lion King and Aladdin were must see animated events because they were epic. Pooh is not.
Thirdly, the "Winnie the Pooh" franchise has gradually shifted from being marketed to the family to being marketed towards preschoolers. Seriously, thats the demographic Disney targets for most of their Pooh merchandise. So many older kids probably didn't want to see the movie because they felt it would be embarrassing or too childish. Deep down they know they like Pooh, but because Pooh has developed such a kiddie-targeted reputation over the years many older kids don't want to be caught anywhere near a "Winnie the Pooh" showing.
And lastly the film doesn't contain modern, hip, pop-culture referencing humor that is so often used to lure people into seeing a movie nowadays. While this is extremely refreshing, it may not be exactly marketable. I feel part of the reason Tangled did better than the Princess in the Frog is because the marketing made it look like a Shrek film where the Princess and the Frog trailers aimed for a more traditional feel.