I don't know. I actually had an idea for an arc in Firefly if it ever returned:
After the whole situation with the Miranda broadcast, the crew of the Serenity become sort of mythic Robin Hood like figures. One day, they meet this kid who was a student at the acadamy with River. He had heard the story of the Serenity, and was inspired. He escaped, and has been on the run ever since. He, like River, is a genius with psychic abilities. However, his psychic powers are not as well developed as River's. Also, while he is skilled in electronics and mechanics, his specialty is that he is an amazing pilot. So, he becomes the ship's new pilot. Now, he is crazy, but not in the same way River is. He's lucid and cognative, but he's still obviously out of his mind. He's Deadpool crazy. This is an example of Deadpool crazy if you're not familiar with it:
http://img141.imageshack.us/my.php?image=shoryuken5jh.jpg
He sort of takes over as the comedic releif, but is a different kind of funny as to not seem like a cheap Wash ripoff.
Throughout the season, we see a new operative tracking the crew. He's often seen watching them whenever they stop down in a town, and ocasionally speaks with alliance oficers in the towns where he's tracked them to. He's fought them a few times, and each time has almost been testing them. He seems to posseses inhuman reflexes, can leap great distances, and has been shown to be able to move objects with a thought. He's also been shown causing violent migranes in others by looking at them. It is quite possible that he is the final result of the Acadamy's goal.
Throughout the season, we ocasionally see him speaking with the new pilot, suggesting that he is a plant on the ship, or is somehow connected to the new operative. The new operative often says that the crew would no longer trust the pilot if they new the truth, suggesting that there is more to the young pilot's past than we realized.
In the season finale, the new operative apears on the ship and starts taking them all out one by one. He cripples the ship, and defeats all of the crew. He then reveals who he really is.
The pilot.
Yes, he and the pilot are one and the same. To insure that he wouldn't blow his cover, the Alliance programed a case of multiple personality disorder into his brain. He locks up the crew, and puts the ship on a course to be intercepted by an alliance cruiser. There is only one obstical left.
River.
River establishes a telepathic link with the pilot, and begin to battle furiosly in the physical world while calmly talking in the world of the mind. Eventually, the battle shifts into one between the two personalities, and with the help of River they are eventually fused together into one personality. The new personality has the inherent morality of the pilot, his sense of humor, full control of the operative's skills and powers, and a darker nature. The two of them fight and kill the alliance operatives, and free the crew. The pilot then leaves to be seen again another season.