If you are going to manually select for better mitochondrial DNA, what's the difference between that and manually selecting every other bit of DNA.
Sure, we select DNA when we choose a mate, but when you're twiddling with it below the cellular level what's keeping people from custom babies? Allowing *just* this will permit for a race of super men, bred for their superior metabolism by simply selecting better mitochondria.
"But this is for fixing a specific disease." Sure, but that doesn't make the results any different. You engineered a "better" baby. Why can't anyone else do that. What makes you and your broken DNA special? I want to engineer out acne & BRCA mutations. Oh, too bad for you, can't pay for custom baby fixing and now your baby is stuck with Alzheimer's. If we're just "fixing" things with babies, red hair is a "defect", let's remove that and replace it with blonde...
IMO, allowing this is a slippery slope.