I'll cut off the sweet talk beforehand and get straight to the point here:

With Shepard being an established character in the ME universe, but their background, modous operandi, and actions throughout the game being largely up to the player, would Shepard count as an OC or not?

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That... is a complicated question, that is further complicated with Biowear stating that some choice and endings are canonical.

I've seen only one piece of fanwork that touches on that, and it was an excuse to have the Master Chief stand in for Shep