2D movies just don't fit this era anymore. Sanzaru made that animated short film. Even with more frames like old Disney movies, the movie doesn't have the cute factor like it has now.
To get non-gamers to see this movie they need that cute factor with fuzzy animals. Bentleys eyes are probably visible to make him more likeable. People look at eyes first, when you can't see them.. there is no trust in them.
The choices they've made are probably all marketing. When I have to create a 'game design document' at school, we always looks at estimated ages that will be playing the game and see what fits the best. Recently we started working on a game that can teach you a new language through playing. We chose a Knack/Pixar kind of style because it is timeless. People love it and its totally now.