Even if Gilgamesh is arrogent in this battle, it won't really matter, as the weapons from his Gate of Babylon is more than enough. (Homing weapons, healing negation, GAE FRICKIN BOLG.)
I thought Gilgamesh couln't use Gae Bolg's sure-kill curse, because it's a weapon meant for close quarters, and Gil just fires them like rockets. But he does have Fragarach, which is the same, except it can be thrown.
But anyway, I'm also going with Gil, he speed disadvatage is just too much. In the UBW route, Gil was defetead by Shirou because he could project weapons faster than him (also because Gil is stupid and arrogant as hell). In this scenario, there's nothing stopping Gil from flying in his Vimana and shooting swords from the sky like meteors.
On the other hand Cloud has good attacking power and durability, and if he manages to strike a couple of times, Gil would take great amounts of damage.
In the end, I'm giving it to Gil, because of higher speed, versatility and hax.