IMO Kabuto wins because of all his techniques such as sound genjutsu. Ability to attack using inanimate objects, extreme regeneration abilities and a solid defence through the use of Suigetsu's and Kimimaro's techniques.
Kabuto is also extremely intelligent and could figure out how to beat Pain. He also has white rage to blind the paths making linked vision useless. A bansho tenin is pretty dangerous as Pain can use that in unison with human path to take away Kabuto's life but Kabuto can use some of his various abilities to avoid being pulled.
CT is a problem but Kabuto would survive it by turning to water and having bones stick out. Getting out of it is a problem though....
Conventional attacks such as chakra rods, animals and mechanised weaponry is quite useless against Kabuto though.