IOW, Gil has all those weapons in the King's Treasure Vault, but he doesn't know them. He's the kind of man that sees himself as too great to need to learn such things. That's why his use of the Gates is mostly firing the weapons out at great speed, without even actually using the weapons. Only rarely does he actually deign to pick up a weapon other than Ea, and when he does, it tends to be because he wants to humiliate his foes. His overblown ego is EVERYTHING.
UBW is kinda balanced when you realize that 1) it costs prana (quite a bit) to activate and to keep up, 2) it costs prana to duplicate weapons, 3) it can only duplicate weapons that Shirou/Archer has encountered before, 4) copies are always weaker than the originals, and 5) it can't duplicate non-weapons without a significantly higher cost.
Really, if Gil hadn't gone with Gates of Babylon, Shirou wouldn't have had any chance whatsoever against him.
edit: Really, I don't think this is so much a plot-hole issue as it is a case that Nasu hasn't explained it very well yet.