There’s an interesting pattern in the mtDNA of archaic humans. Neanderthals have mtDNA that’s a lot closer to that of anatomically modern humans than to Denisovans, although Neanderthals and Denisovans are close if you look at nuclear DNA. While really ancient mtDNA from Atapuerca is like Denisovan DNA.
People now suspect that there was a bit of contact between Neanderthals and AMH a long time, maybe two interglacials ago, contact that led to a mtDNA lineage from AMH humans being introduced into Neanderthals – one that spread until all (or almost all) Neanderthals had it.
This kind of thing is especially likely to happen with mtDNA, because there is reason to suspect that Neanderthals had crummy mtDNA.
The first problem is that there may not have been enough Neanderthals. Selection is not very effective in removing deleterious alleles when their selective disadvantage is < 1/N. For Neanderthals, some analyses indicate the effective population size was around 1000 (others think it was a large but deeply subdivided population), but the effective pop for mtDNA (haploid and only transmitted by females ) was 1/4th that – so, N ~250. Not very big.
The other, general, problem with mtDNA is lack of recombination. In an asexual lineage, mutations accumulate. Muller's ratchet. The only fix is back-mutation, which is very rare, unless the species population size is huge. Sex, on the other hand, reshuffles: a kid can have fewer deleterious mutations than either parent.
So you don’t expect hominid mtDNA to be in great shape, nearly perfectly optimized. That’s closer to true for nuclear genes. Since hominid mtDNA is not too close to optimal, it’s not a huge surprise if population A has noticeably more effective mitochondria than population B.
Since mtDNA also does something very important, Neanderthal mtDNA being replaced by AMH mtDNA isn’t particularly surprising. Along the same line of thought, zero success of Neanderthal mtDNA in modern humans is also not terribly surprising. Neanderthal and AMH mtdna being so functionally close as to be effectively neutral – now that would be surprising.