Super Shadow, probably him. Regular Shadow, probably Cloud.
@ulitmateninjagaidenx: Cutting through steel towers with ease, deflecting bullets while simultaneously handling someone with super speed, tanking blows that shatter steel without any signs of harm, being thrown through several feet of steel without any signs of injury, levitation, can cut through somebodies soul, cut through anything, launch blade beams, create powerful gusts of wind, paralyze people with a strike, etc. etc.
I still don't see how Shadow is even going to hurt Cloud.
And though his speed is great, it has been stated multiple times Sonic is only a a Mach 1-2 Speedster outside of Super form, and Shadow only matches Sonic, maybe slightly faster at times. Seeing as Cloud can easily deflect bullets from multiple sources, which each move Mach 3 or better, I don't see why Shadow's speed would be too much of an issue. And even if he does hit Cloud, I doubt it'd even hurt him, it'd probably just inconvenience him slightly.