[Village Idiot]

The reason why Shirou was able to defeat Gil was because UBW is the direct counter to the Gate of Bablyon.

Gil's weakness is that he is not skilled with any of the Noble Phantasms that he possesses, so although Shirou/Archer's UBW replicates objects that is weaker than the original, it also Traces the memories of the people that once welded them, automatically making him a master of anything he uses.

Gate of Bablyon's other weakness, is that once all of its contents are released, it's effectively useless, while UBW can keep on replicating more and more copies of the same Noble Phantasms as long as Shirou/Archer can keep UBW up.