I am glad the bubbles helped Derpy and this is definitely an original way of looking at her past but it is extremely to lacking in context for this to be the entire story. Some big, obvious questions come up. Why is Derpy sad? Who or what are the bubbles? She doesn't have a clear background before this small story of her journey through the Everfree forest. I'm glad that the bubbles are helping her but I don't understand the reasons for any of it. She's just suddenly crying in the rain, presumably lost, and suddenly some glowing bubbles take pity on her and lead her to ponyville which seemed to be the only meaningful bit of the story as I had no context to why she was out, lost in the woods in the first place. I felt a bit lost at first, like I was only coming into a story half way through.
Storyline criticisms aside, the script work seemed a bit faulty at times, the "Timber wolves'" collision boxes seemed to only function occasionally and Derpy often times ran off into thorns or other obstacles she shouldn't have been able to once scared as well as her AI being exceptionally dim, even for being a clumsy, cross-eyed pegasus (which is a trait that seemed to be missing by the way). The levels themselves seemed a bit easy despite this AI wandering around and not realizing the light had moved to a place to the side of her (thus, walking through a wolf that didn't do anything for some reason) and the number seemed to be a bit low as well. You could have made a few decent puzzles from the mechanics (opening pathways with tripwires, moving platforms, ect.) you introduced but sadly they went on underused. The art and music were great though and made the game quite beautiful in a somber, angst-y way. It was enough to bring it from a 2 to a 3 so thank your artists and see if you can brush up on your coding skills and talk with some other flash devs to see where you might improve.
Also... Brohoof! /)