Well, Cloud is more versatlie. Between powerful slashes, potent equipment and magic spells he can keep Raiden on the ropes. But Raiden still holds the strength and endurance advantage (Meatl Gear Ray and Excelcius and Armstrong's strikes), along with attack speed (I heard that his slashes in Blade Mode break the sound barrier) and weapon efficiency (HF Blades are crazy powerful, but we can't teell for sure if they can cut through Cloud's sword). Add the arsenal he holds in his hammerspace (smoke grenades, regular grenades, EMP grenades and bazookas, oh my!) with The Ripper and Cloud has a lot to compete against. I am unaware of Cloud's full potential so I'll keep an open mind.
A team-up is another story. Can't figure out how it would work, but it would be FRIGGIN' AWESOME!
Yeah, difficult to compare these guys. Both awesome, both OP, plus they come from two different universe styles (fantasy and sci-fi respectively) so the outcome of a clash would be totally unpredictable.