I personally think Shepard > MC
But tell me what you think, and if you think MC > Shepard then tell me why you're wrong?
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Chief gets shit done, no real questions asked. Like a badass. Shepard bangs his through the galaxy (and the decks of the Normandy), asking all sorts of questions, getting to know everyone and helping in lots of little knit-picky situations/fetch missions. If I've gotta have one to save the galaxy? Chief. Durr. Can you imagine if Chief was calling the shots on the Citadel there at the end?