Fate/Zero

[Xelbair]

Gil vs Shirou in FSN? There's no way he would have taken him seriously. Either you meant Gil vs Saber, or you meant UBW instead.

Gil vs Shirou in UBW - Shirou won thanks to three things:
1) he had access to excessive amount of mana(from Rin)
2) He knew how to wield those weapons properly.
3) Gil had limited mana(he had to feed on humans to gain it, grail wasn't keeping him in this world, and mana from Kotomine(if he got any) wasn't enough)
Basically Gilgamesh has grand armory of weapons, but he doesn't know how to wield them - even if Shirou's weapon got destroyed he just projected another one - and thanks to training with Saber/observing Archer he was pretty good with swords.
Plus he is arrogant as fuck - if he used Ea vs Shirou, it would be instakill.

[Archangel]

Gil vs Shirou in UBW - Shirou won thanks to three things:
1) he had access to excessive amount of mana(from Rin)
2) He knew how to wield those weapons properly.
3) Gil had limited mana(he had to feed on humans to gain it, grail wasn't keeping him in this world, and mana from Kotomine(if he got any) wasn't enough)

1) Excessive is the wrong word, he had enough to use his weapons.
2) Not properly, just better than Gilgamesh. There's a reason why he kept himself in range for close combat as well, it denied Gil of the possibility to use his power as the Archer class.
3) This is just wrong in every way, Gilgamesh had infinite mana as he was being fed directly from the grail.

Oh and 4) the chains we saw weren't usable against him in any meaningful way because they're made to hold divinities. As we saw it in the UBW route, they were just normal chains when used against Shirou.

But the bottom line is what everyone's been saying all along, he was arrogant and conceited which eventually brought his downfall. His pride would have never allowed him to go all out against a human from the get go.

Gilgamesh doesn't even take Saber that seriously in FSN. He sees her as a feisty cat to be tamed, not as a worthy foe. Only inside a Reality Marble could Gil use the full power of Ea, since it destroys worlds. Thus, he never unleashed its full power.

He's as arrogant as ever around her but he does take her seriously, otherwise he would have never have used Ea against her.

PS: You know, this is total bulshit. I could have been surprised by Berserker's identity if that ending of him standing in front of a lake in season 1 hadn't completely ruined it.