I was more disappointed by the Shepherd's death, as I think he had the more mysterious and interesting backstory. There had been hints that Wash was doomed in the first season episodes that were shown... for instance, in the episode shown on SciFi last night, Wash and Mal are captured and tortured. Wash was clearly shown to be a "weak link", good as a pilot but not a tough fighter on the ground.
As for Shepherd Book, there were lots of hints in the series that there was more to him than he let on. There was some hints in the movie as well, during his conversation with Mal when the ship stopped at Haven (before the planet was attacked). I would have liked to have seen what got the Shepherd to leave the ship and settle on Haven...
I think the first season of "Firefly" would have ended with the revelation of River's true nature as a living weapon; there were lots of hints in the series but nothing definitive was said in the episodes filmed. Season 2 would then have revolved around the growing threat of the Reavers, ending with the revelation of how they were created. I think any follow-on movies will be about the growing destabilization of the Alliance, possibly leading to a second civil war...
End spoilers!
I agree with your ideas. I'm wondering if The Shepherd was something like The Operative in his life before he became a Shepherd. His character reminds me of Brother Cadfael, who was a Crusader before he took the cowl in his early 50's.