Yeah...really late with this:
So uhh, I have to challenge multiple points here. 1: how is Shirou a villain? His primary driving goal going into things is to save as many people as he can, and this changes as his character develops across the three routes. 2: Kiritsugu could qualify as a villain, but is really more of an anti-hero. Vaguely noble goals, awful methods. 3: Do... do you know what a fascist is? 4: Rin is just straight up a good person who was raised by an absolutely awful person, so thinks she needs to put forward a hostile mask.
1.
I'm very curious as to why people think Shirou suffers from sloth.
Because there is a specific manifestation of sloth that occurs when a person just endures a set of circumstances without being willing to change them while trying to help keep as many people as possible alive. Usually a soldier in wartime who is a good comrade and warrior but is unwilling to confront the system itself that left him and his comrades on the battlefield that is killing them.
There is a difference between saving people and protecting people. Shirou will jump at any chance to save someone, but will never protect anyone, himself included, from the world or himself. This is what makes him such a tragic anti-villain. Think about all the times Shirou saves people, helps them continue existing, but never helps them to live their lives.
When has Shirou ever personally actually helped anyone, himself included, overcome their problems instead of just beating them back for a time?
2. No. Kiritsugu talks the talk of an anti-hero, but he doesn't walk the walk of an anti-hero except in the nominal hero sense since he is the POW character of Fate/Zero. Again like Shirou Kiritsugu doesn't protect anyone, but unlike Shirou he also kills people to get what he wants intentionally.
3. Which type of fascist?
Fascist? Villain? Shirou? I agree that his main problem is sloth, being unable and unwilling to move past his father's death, and being unwilling to adapt his ideals. Ultimate Blade Works is this personified, allowing him to create derivative works that can overpower the original.
But I wouldn't call him a villain or fascist. Shirou is too dedicated to heroism. He's a person who always chooses to sacrifice himself for the greater good and always will fight against the greater good if it demands the sacrifice of others.
I don't say this to aggrandize him, but he is not a villain, i belive a brighter world would allow him to live up to his ideals while also helping him move on.
Would a darker world not punish for his attempted heroism?, or crush him before he could do any good?
Because Shirou is a brownshirt: Someone willing to fight a war for another's ideals unquestioning because they appeal to him.
Kiritsugu on the other hand is an out right full fledged fascist who kills the other/tainted/evil to get the power to change the world to his violent liking.
4. No. Rin is someone with a veneer of being a good person, in front of herself even, but when it comes down to it she doesn't have friends. Only comrades, rivals, lovers, subordinates and superiors and , like with Shirou, Rin will save people, but she won't protect them.
I'm vaguely curious what fanfic you read and internalized as canon, because there is no canon Avenger Emiya whatsoever. EMIYA Alter is a version of Shirou that ties into Kiara Sessyouin and broke there, completely unrelated to the UBW route. And he's an Archer, not an Avenger. The only thing I could think of that comes close to an Avenger EMIYA is Angra Mainyu in F/HA, but that's not EMIYA or Shirou, that's literally just Angra Mainyu pretending to be Shirou as he uses Shirou's body. Also, Archer is always dead at the end of the UBW route. Well before the end really.
It's my headcanon/persistent brainfart. As in every time I think of Emiya Alter I think of him as an Avenger even though he's still an Archer.
This is because I don't actually know that much about the guy other than killed Kiara Sessuyoin's cult in his timeline and wants her perma-dead which resulted in him walking the Path of the Heretics/Madou which makes him basically a type of Oni produced by murder which fits better in the Avenger class in my head.
I... what? So uhhh, I might be mis-remembering, but by the time Kiritsugu confronts 'Irisviel' in the 4th Grail War, Iri is straight up dead, and that's a simulacrum Angra Mainyu formed out of the grail mud. And further, you're ascribing a lot of very complex theoretical and medical competency to an assassin. Just because he has an affinity for something doesn't mean he has the knowledge of how to do it.
That is exactly my point: Kiritsugu is just an Assassin. Even after he learns that his beloved wife is going to die and from what, he doesn't bother to try to learn the knowledge needed to save her life or to find someone who has it to help him. If Kiritsugu had medical knowledge or just straight up got a doctor/surgeon hired or hypnotized to help him separate the Grail from Irisviel she wouldn't have had to die.
Remember that the Holy Grail war always takes place in places with a lot of leylines so Kiritsugu had the option of at least trying to carve Irisviel's heart out and hooking her up to a leyline as a form of life support. If it had worked it probably would have resulted in an Irisviel possessed by Angra Mainyu at the end of Fate/Zero because all the leylines in Fuyuki are connected to the Grail, but Kiritsugu didn't know that and he didn't even try.
I'm not sure where you're getting the idea of Shirou damning himself through Sloth, because uhh, no, that's kinda absolutely not his thing. EMIYA made a deal with Alaya because he was too motivated to keep saving people, not through apathy or laziness. As to making their own swords... when you pick up the contents of the Gate of Babylon, and all sorts of random other shit, what exactly are you going to make yourself to surpass that?
Again, there is no Avenger EMIYA, though it it sounds vaguely like you're talking about EMIYA Alter (an Archer), who condenses he reality marble into a bullet and shoots it into people, and then lets the swords explode out of it, but there's not really anything cancerous involved, and it's pretty damn targeted.
It overall reads like you read a bunch of dark fanfics and conflated those with the original source material, and it's making you take a significantly harsher view of the characters than is really justified.
Shirou himself at one point notes before fighting Gilgamesh in one of the routes that every other Servant summoned in the war would be a problem for him because they have mastered their Noble Phantasms, but Gilgamesh never mastered any of the ones in the Gate of Babylon so he can take him.
In all versions of the Fate stories it never occurs to Shirou to master any of the Noble Phantasms he has copied or to make his own. He instead makes an inferior copy of the Gate of Babylon and modifies some Noble Phantasms to serve his needs better, but he never masters any.