Not only that, but since the mitochondrial DNA only codes for a small amount of the respiration chain -- cytochrome C oxidase, ATP synthase, and some of the core proteins of the NADH reductase complex, in most eukaryotic cells -- while the nuclear DNA codes for much of the rest of the proteins in the respiration chain, you need to have an excellent match between proteins that come from two different chunks of DNA. There's no guarantee that'll happen, and there's evidence that one of the reasons cloning has such a poor success rate and so many cloned animals die young of strange damage, is precisely because of poor matching between mitochondrial and nuclear dna products, leading to oxidative damage throughout the cell and early cell death because of leakage from the poorly-functioning respiration chain.
Man, once our genetic engineering is good enough, one of the first things we should do is migrate those mtDNA genes into the nucleus, already, and get them working under proper sexual reproduction/selection. Clean that shit up.