According to the Shepard's Tale comic, which reveals his backstory,I'm not sure it's a question of good or bad it's a question of freedom/anarchy versus restriction/good goverment, Simon, River and Inara all actually supporting the Alliance in the war, Wash and Jayne not really seeming to care much and Book...?
he was a high-ranking Alliance operative who was dismissed after a disastrous battle... but in fact, he was undercover all the time, working for the Independents.
The comic is great, I advise anyone who hasn't read it to not open the spoiler and read the comic instead. It would have made an awesome flashback/non-linear episode of the show.
I think the two shows are of about the same quality. Which would mean that, among Whedon fans, Dollhouse is underrated and Firefly overrated. Both shows suffered from being cancelled too soon; Dollhouse had the time to wrap up the most important storylines, in mostly satisfactory way, but that meant that some characters' stories fell to the wayside (Claire, Dominic) and some things were rushed, with entire stories happening off-screen between the penultimate episode and Epitaph Two (Alpha's journey from villain to hero, Echo/Paul relationship). Firefly, on the other hand, didn't even get to develop a story in its only season, though Serenity, the movie, did have an epic story (and is probably what the next seasons of the show would have been about).I like Firefly but i must admit I don't understand the slavish fan devotion towards it, I think it's very much the least of any of Joss' shows, Dollhouse is far superior
For the story, I'd go for Dollhouse; Firefly's strength is in having a lot of likeable characters, which is probably why people get attached to it so much. Dollhouse's problem is that most characters were either 1) dolls, which meant that for a long time they were barely characters in the usual sense of the word, changing their personalities every weak (which later does change to an extent, especially with Echo), or 2) people running the Dollhouse, i.e. morally corrupt people engaged in a form of human trafficking/slavery/violation of a particularly troubling kind. But that wasn't a failure of the show, it was simply the consequence of its premise. However, as the show went on, I thought they did a good job of fleshing out both sets of characters and making them more relatable.
On Firefly, all the characters were interesting and likeable in different ways, and there were no non-entities of the Harry Kim/Travis Mayweather type. However, since it lasted just one season, we didn't get them see develop, the way we did with characters on BtVS and AtS, which is why they don't match the Buffyverse characters in complexity. But they might have - who knows.
On the other hand, Firefly had a very strong start (stronger than any other of Whedon's shows, and than any of the modern Trek shows, for instance) but if Firefly had lasted, for all we know, people might have also started complaining about the directions of the story that they didn't like, and the quality might have gotten more inconsistent... and then maybe people would be saying "oh season 1 was so awesome, if only Firefly had ended then I'd consider it one of the best SF shows of all time, but then they did _____ in season 3, and ruined everything in season 4..." like many say about BSG, for instance. Or maybe there would be people who would say that seasons 5 and 6 were the best, while others would say that they don't recognize anything after season 3.
We'll never know.