Actually come to think of it they fill two almost completely different roles so it's hard to say who is "better". Master chief probably wouldn't have the charisma to unite a ton of races to combat a greater threat, and Shepard would probably have a tougher time taking down all the enemies MC has to fight, like brutes, elites, and hunters. In a direct fight, Chief would probably win, but Shepard is more than just a soldier engineered to kill and then kill some more.
So basically yeah doomguy would win.