riddle me this: if Cerberus could clone Shepard for an organ donor, why did they not just clone Shepard? Especailly since Shepard loses their scars in the process. You could legitimately never tell Shepard they're a clone, and just say a few things were lost during repairs, such as fingerprints, so systems need to be updated with their new genetic identity. It also would have probably cost less.
It really just comes down to TIM being obsessed with Shepard. It's explained in the game (through logs and talking to Miranda) that he wants Shepard brought back exactly as they were before being spaced. He wouldn't even let Miranda put a control chip in their brain for fear of it changing their personality somehow.
It's like TIM thinks Shepard is the peak, exemplary human and he was willing to pay any price to make sure that didn't change.
