The conquistadors were hard men who were highly skilled in close quarters fighting. They did have guns, but at the time most of the fighting still happened with hand weapons -- and their armor and tactics were designed to counter hand weapons. The conquistadors were much, much better at close quarters fighting than the natives. We don't know what stormtrooper armor is supposed to protect against, but it ain't knives. Modern body armor would be equally ineffective. The conquistadors also rarely allowed themselves to be caught in the open (and when they did it, it didn't end well for them). And they usually had the help of thousands or tens of thousands of local allies. My biggest complaint with the movie was that there doesn't seem to be any reason to expect that the imperials would be caught unaware. They seem to be scouting very heavily, then, bam. Everybody line up to embarrass the rebels. And the "legion" seems to only have a few hundred men.