Fate/Stay Night: Shirou's plot armor

One cannot talk about "plot holes" without mentioning the plot armor that Fate/Stay Night gives Shirou.  First, no, I am not salty because I'm a Gilgamesh fan.  Hell, I have hated this plot armor ever since I've watched UBW (without having watched any other Fate series prior) and before I became a Gil fan.

1.  Shirou vs. Gilgamesh fight:

The story can go on and on about how "Shirou has absorbed Archer's skills" and "Gilgamesh lets his pride get in the way" all it wants.  It would be believable if the story let Archer win against Gilgamesh, but not Shirou.  And here's why:

• Even Archer would have a bit of trouble defeating Gilgamesh.  Shirou - who would lose to Archer in a fair fight (reminder: in his fight with Archer, Archer let him win) - should in no way defeat Gilgamesh. Shirou has gained UBW but his agility and skills were lacking; he was someone who didn't even know how to sword-fight 2 weeks ago. Meanwhile, Gilgamesh is famous for many forms of combat, battled gods and demons in his life, can manually use all the weapons in his GoB, single-handedly supplied several Servants at once while protecting Uruk with a magical barrier. Yet FSN dares use the excuse that "Gilgamesh is a king, not a warrior" (Hello, he is both!) for why a high-schooler would defeat him in swordfight. 
• Gilgamesh isn't an A-rank melee combatant. But GARcher himself isn't an A-rank warrior at melee combat, either.
  Gilgamesh < Lancer in melee combat.
  GARcher < Lancer in melee combat.
  Shirou < GARcher.
• While UBW is a decent counter to Gate of Babylon, Shirou can't realistically physically keep up with Gil due to Gil being a demigod and Shirou being a human.
• Gilgamesh had 2 perfect chances to kill Shirou and co. when they were face to face before the showdown:  in the first instance: Shinji stepped in (as if Shinji had any importance to him);  the second instance, Gilgamesh has opened a dozen Gates of Babylon about to launch but the story doesn't forget to have Rin threaten to shoot Shinji as if she were a threat. Gilgamesh himself said that even if she killed Shinji, it'd be no problem to him. Yet he went, 'Ahhh, I've opened a bunch of GoB but I'll withdraw for now 'cuz I don't want dust on my clothes' - haha... what a ridiculous reason! This is the person who had crawled in dust to battle many things in his life. Not to mention that retreating is totally not Gilgamesh's style.  
• UBW itself is a huge mana cost, while GoB costs much less mana and has the most powerful weapons in the universe.
• The weapons projected by Shirou are B-rank so they shouldn't be able to shatter Gilgamesh's A-rank weapons. It's only wistful thinking that UBW can match GoB:  GARcher, while having Rin as a Master, could only take half of Heracles' lives and died in the process. Gilgamesh, while having a crappy Master like Kirei, took all of Heracles' lives effortlessly.  
• Even if Gil didn't want to use Ea, he has numerous magical weapons in his GoB. Yet he only used swords against Shirou. Shirou is able to trace things that aren't swords but it's much more costly for him. Gilgamesh could have easily overwhelmed him with things that Shirou can't replicate repeatedly or replicate at all. 
• The number of times you see Gilgamesh shooting hundreds of weapons from his GoB and suddenly he couldn't hit Shirou.
• The story never shows Gilgamesh in his golden armor, even in his fight with Heracles, because it has to make him look as vulnerable as possible.

2.  Shirou vs. Kirei fight:

Shirou is also shielded heavily by plot armor in his fight with Kirei.  Did you see Kirei vs. Kiritsugu fight in Fate/Zero?  That man fought like a demigod against Kiritsugu - who was an experienced assassin and well-versed in the defense art himself, who used Double and Triple Accel and still couldn't "get" Kirei. Shirou is a lesser mage and a lesser fighter than Kiritsugu, is simply no match for Kirei.

This is a pretty typical hero's journey BS where the protagonist wins by plot armor and a lot of dumb luck.