Well, I'd say the link between humans and apes via genetic, fossil, an physiological simularities has been conclusively proven. We have ape bodies, ape genes, we have a series of ape fossils that become progressively more like us. The case that we are apes is pretty solid. What we can't deliver is an exact account for every single transition from the nearest common ancestor of chimps and man to modern man and all the evolutionary dead ends. This is because protohuman fossils are rare, which is unsurprising for species that existed with small populations over short perioids of time. But there's no reason to think that we need to understand every transition to conclude that humans are decended from and indeed are apes.