The DNA evidence of our common descent with chimps has only grown stronger after sequencing the genome, so your reservations about this story are based upon a misconception.
Rickets. LOL. Yeah. Like leper colonies. In the stone age. With dinosaurs presumably?
According to both morphology and DNA, neanderthals are distinctly not homo sapiens.
The MtDNA had little relationship to modern human MTDNA, but now we are talking about the genome inside the cells ~ not just the mitochondria.
The Neanderthals are exceedingly closely related to Europeans and Eastasians.