A good trope to subvert, sir!
I think the bias comes from the political implications of the title Emperor--the reigning monarch of an empire.
"The term empire derives from the Latin imperium (power, authority). Politically, an empire is a geographically extensive group of states and peoples (ethnic groups) united and ruled either by a monarch (emperor, empress) or an oligarchy." -- http://en.wikipedia.org/wiki/Empire
That an empire is a "geographically extensive group of states and peoples (ethnic groups)" implies that these states and peoples were conquered. That's usually how it happens, anyway. I can't think of any political entity referred to as an Empire which did not acquire sovereignty over its many states and peoples by conquest. So, an Emperor has either forged or inherited a state which willingly suppresses the sovereignty (and usually oppresses the people) of the states around it.
From this perspective, one might argue that the only good Emperor is the one who dismantles his Empire, apologizing as he goes.
An exception would perhaps be in a situation where the imperial subjects across the world (who are well-treated, we must assume) realize the need to unite for protection or to accomplish some goal. In this case, the Empire would still have been an ill-gotten creation, but the good Emperor doesn't dismantle it because at present, nobody wants him to.
I think they are the main reason why Emperors are used as the evil bad person.
I try to avoid using cliches in every way possible, since I sometimes have a tendency to use them. But with the whole government thing, I use a different government for each race. The Aeloo have a council, the Toxati use a system similar to the United States, and the Sheniolaens practice tribalism. 