I don't consider this fan fiction. I consider it more of fans getting together and making a quality script worth reading.
I kind of see what you're saying. Instead of being more of a fan fiction, this is a bit more like active artistic accreditation with team involvement to understand and follow through on what it's like for the actual Futurama team to develop an episode by engaging in the same processes to produce a more professional style script.
I also assumed from your earlier starting presence of the Professor discovering that the Universe is shrinking (a pretty good idea for a premise) and with Nibbler's much needed human form transformation, that it would be a little obvious that the PE crew would visit spheres through the new invention the Professor invented. Most stories generally have a foil to the protagonists, although not possibly evil, I assumed that Professor Cat (from That Darn Katz) and Dr. Banjo (from that episode with Dr. Banjo in it) would help team up, possibly with the Porno Dealing Chameleon (but I didn't want to shoot off too quickly) to insure nefariously that the Professor (from various episodes containing the Professor) wouldn't be able to determine why the Universe was shrinking in the first place. At the ancient alien landsite, you could probably introduce Fry, Leela, and human Nibbler in a comical setting because of Three's Company, and the Professor and Bender (from every episode of Futurama ever) play up as a Mr. Roper and a Mr. Furley respectively.
What do you think?