dariusop replied to your post:
Shirou wins because no one takes him seriously. Gilgamesh is noted to be a lousy at sword fights, and he wouldn't take on anyone he knew to be more skilled than him in one. Gil was held back by his hidden E-Rank Phantasm - Immense Ego
Well, Shirou and Gilgamesh are the polar opposites in that regard. Most (not all) of the fights Shirou wins/escapes are because no one takes him seriously or because of Avalon/luck(Lancer/Gilgamesh/Rider) yet most of the fights Gilgamesh loses are because HE won't take anyone seriously (Saber/Shirou/Sakura).
adelusionaryexistence replied to your post:
Except Dark Sakura.
Not really, he could skewer her properly if he really wanted to. His ego made him underestimate how fast she could heal herself and devour him. If he was a mind similar to let's say, Kiritsugu's, he'd have obliterated her and she wouldn't have managed to understand what/who got her. Her body is only human. And he has the power to do that.