A developed story with something to grip the audience is always an added bonus for a Flash film. You can't have a very developed story in a film that is one-and-a-half minutes long, normally, but you should try to grip the audience. A good way to do this is have a mixture of dialogue scenes and action scenes. People often think good action films have 20 minutes of mindless explosions in them. The truth is, that is not the case. The 2007 Transformers film is a good example of a film where the action scenes are a bit too long and excessive and many people who watched the film lost interest during the intense, long, explosive scenes of action. Titanic, meanwhile, kept the interest going even during the hour or so of mindless action as the ship was sinking, because of the fact that there was always a focus on the characters saving eachothers lives and their reactions of the boat plummeting to the sea, unlike in Transformers where it was almost a destructive fireworks show with no focus on characters.
In terms of Flash films, though, a good example of keeping the interest going with a mixture of action scenes and quieter scenes is the Brackenwood series. With the exception of the Yu Yu, which was just a three-minute action scene, although the films have no dialogue other than the noises the animals make, the Brackenwood films have a mixture of scenes such as Bitey jumping through the trees like Tarzan and scenes which are more quieter, such as characters getting annoyed with one another.
If you have never thought much about story structure and things like that, I hope that that has interested you.