That is actually fairly simple: The machines DO grow the humans out there in the real world (please, don’t get into the matrix-within-the-matrix now, thank you for your corporation). How we look on a basic level is a question of genetics. The machines can just read the genetic code, program that into the pod-humans digital self… and voila. “He has his father’s eyes.”
Which is why Neo does look like Mr. Anderson. And vice versa.
__________________ "Those who can make you believe absurdities can make you commit atrocities."
-Voltaire
"That includes ruining Halloween because someone swallowed a Bible."
"I just thought you were a guy."
"... Most guys do."
I have to agree with Omega here.
Surely if the AI is advanced enough to create the Matrix, then they have the technology to read our DNA (genetic code) and then duplicate that code in the Matrix so we look the same there as we would in the real world.
While i agree with Ushgarak to some extend i dont think its that they programmed everybody in my opinion all they did was something like what they use now days to find criminals, sometimes seen in Americas Most Wanted all they need was to take a picture of any person then advance it so theyll know what they are gonna look like and then program it since now they know what they look like
__________________
"A lie, Mr. Mulder, is most convincingly hidden between two truths." Deep Throat.