Greetings!
A Pipkin-centered fanfic sounds like a very good idea, given that he's never actually been portrayed as the protagonist alone - usually, he's the innocent sidekick of Hazel or Bigwig.
How about this: Set sometime during the TV series, curiosity gets the better of him and he ends up getting captured by some human and kept as a pet. During that time, he befriends one of his human captors (preferably a child rather than an adult), who eventually ends up helping him escape. Basically, the story will be about Pipkin undertaking a long adventure through the human world and also learning that sometimes friendship can even be found in your supposedly worst natural enemy...
How's that for a scenario?
On a side note, I've used Pipkin in my WD fanfics The New World, mostly as he's portrayed in the film and series, only he becomes a close friend to a human protagonist who becomes something of a surrogate father to him. In this story he has his fair share of heroic moments. I won't give away important plot points here, but I can tell you, in this universe the rabbits are portrayed as anthropomorphic, so they can communicate with humans (although many of them speak Lapine rather than English, which creates a certain language barrier). If you're looking for inspiration, you might want to check them out on fanfic.net. Any comments are welcome!
Alex