I don't get the 3 movie thing either, so lets compare the screen adaptation of Harry Potter, which was an abridged version of the series. The adaptations went from 120 to 380 pages per hour of film. An unabridged adaptation of The Hobbit would run closer to 100 pages per film hour, and we'd wind up with a 3.5 hour film adaptation of The Hobbit... or three 1.2 hour movies? Seems like they would need some filler, or longer action scenes, or something.
Concerning the pin....the storyline is well known, and the first film comes out in 2012, so on the surface it shouldn't have any impact, making a good excuse to give the pin custom animation and voices. But this is JJP with an LCD, so actual movie clips and voices may be higher quality coming directly from the film, which would imply all 3 need to be out first... so a valid concern by the OP.
I get the impression that at best JJP #3 is The Hobbit, and I anticipate JJP to run 1 game per year, implying 2014 for any Hobbit pin anyhow, so maybe it's all a non-issue...