RODAN
K so I'll try to avoid going into what goldie does for the Fate route, or his many parallels to Shirou, as those don't really determine whether or not he's a good character in
this show. But suffice it to say we're skimming the surface.
All but the most minor characters in FSN are extraordinary in that their actions are almost completely informed by their detailed, and yet sometimes subtextual, backgrounds. You can even figure out why Shinji is such an extreme shithead, and why Shirou would have been friends with him in spite of it. Gilgamesh is a figure of myth, and while the novel provides a short blurb about him, it never makes explicit the connections between his legend and his actions (Nasu added scenes for Caster to that effect in UBW).
If you don't know the legend of Gilgamesh, here is what is relevant to FSN. Gilgamesh is one of the oldest legendary figures on Earth, supposedly ruling when even Egypt was a fledgling kingdom. Half-god (aren't they all), he treated his kingdom like his garden. To him, all the lands of the world and his people were nothing but his possessions as king. He used and abused his possessions whenever he saw it interesting to do so. The gods saw this and frowned upon it, but rather than punish him, they sent him a friend named Enkidu. Enkidu convinced Gilgamesh that it might be more interesting to protect his possessions from harm, and that there was more fun to be had as a hero.
Gilgamesh was never a character who went from being evil to being good, as he largely predates that popular dichotomy. One day it was interesting to be an asshole, then someone showed him it was also interesting to be a hero. He's never simply greedy; he already owns everything. He's never simply wrong; his place as king of heroes entitles him to be the law of the world. All the world is his garden. He craves experience and we see him sympathize with the unique experiences of others, while detesting those he finds boring. Even FSN insists that the heroic spirit Gilgamesh, who has gone slightly mad through contact with the grail and a decade living among people he finds insufferable, is not evil.
The true grail, Angra Mainyu, represents all the evil of the world. The combined three part story of FSN pits the meager and often self-sacrificial efforts of Shirou, Rin, and Saber against the sum total of all bad things in the world. In UBW, Gilgamesh represents a different force pitted against that evil; cynicism. He wants the world to restart and be built up again "as good as it was in the old days". You can probably see how this is a popular enough feeling that it might be worth addressing if FSN is to be the definitive work on heroism in the modern era.
So while Gilgamesh shares many of his actions with more generic characters, those characters are generally not interesting because they never have a reason for their actions. In Gilgamesh, we can see why a character would conspire to commit murder, attempt to force marriage upon another character, hope to wipe out humanity, and yet also at times show mercy and sympathy for others, and none of this is inconsistent as long as the character's actions are informed by their personality and background rather than being the bad guy or evil.
In general FSN wants us to look past old notions of villainy and see the world's problems as societal rather than anthropomorphised. Gilgamesh in this story is less like a typical villain and is almost a rival antihero; in both Fate and UBW, his goals are perversions of things that Shirou wants (and it's already clearly no coincidence that the two are so similar in terms of fighting). Ok, I am really risking segueing into the Shirou stuff here so I'll stop.