Wow, some nice (even deep!) sociological discussions going on here! I plan to write a paper on the movie/TV series this semester, so the more the merrier
It seems to me that calling the Alliance "communist" or "fascist" is simply splitting hairs; the central tenet seems to be highly organized and centralized government at the expense of local autonomy. The emphasis was on order above all else; other arrangements would be tolerated as long as they didn't disturb the peace. This can be seen in the widespread corruption among Alliance officials, as well as the numerous petty theives and crooks, even in the central planets. As long as there's no major disruption, this sort of behavior is tolerated.
At the same time, it's clear that the Alliance government, though nominally democratic, heavily favors the more developed central planets like Ariel. I imagine this being a sort of bureaucratic bias; the inner planets are more populous, with more representation, and more power in the parliament. As a result, they get the lion's share of the taxes. One can easily see how such an arrangement might have led to civil war.
The "evil" is more of a bureaucratic than a totalitarian evil; bad things are done because they're approved by faceless bureaucrats who never have to deal with the consequences of their actions. The civil war, for example, was clearly a war of conquest, taking back territories held by the Independants. This would have left the parliamentary leaders far behind the lines, free to order heavy bombardments and chemical weapon attacks in the interest of the greater good.
The PAX, in my view, was a way to prevent further factionalism and civil war, to retain the preferential treatment of the core worlds. If people are always happy, what do they care if money and resources are siphoned off? Similarly, when the Reavers emerge, their numbers (about 30,000) are too small to be a serious threat to the Alliance as a whole; the bureaucrats therfore find it convenient to do nothing.
The evil, then, is a faceless evil, the sort that anyone might be succeptible to if granted sufficient power and distanced from the people the power effects.
Jam it back in, in the dark.