Shouldn't the Samehada's traits be restricted as well since it falls under ninjutsu...? Anyways I see Madara winning with high difficulty since Kisame is very strong and quite durable.
I can't quite remember too many occasions of him fighting in close ranges in the manga, when not boosted by Senjutsu. But my gut says Madara's probably quick enough to evade most of Kisame's attacks and out maneuver him.