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The first Machines mown down in the war scene are the most humanoid, and by the end of the battle only the most alien designs are left standing. This ties in to a backstory point mentioned in "The Art of the Matrix": by the time of The Matrix, the Machines are meant to have developed a bigotry against humanoid shapes, with the most human robots falling in to the lowest "caste".
"The Instructor: May there be mercy on man and machine for their sins."
