There wasn't a great deal of evidence in this case, but the evidence that there was all pointed to the parents. The theory that she died in the apartment and the parents covered it up is the most believable and somewhat backed up by evidence. The dogs signalled ONLY in the McCanns apartment and car. Background checks were done and nobody ever died in that apartment before. They washed her cuddle toy and bedsheets. Their statements each contradicted each other. Their behaviour in general and reluctance to do a reenactment was odd. The window didn't open from the outside, Kate's DNA was found on the window.
When Kate first noticed her missing, she yelled "They've taken her". Strange assumption to make when your child has just gone missing
Why the McCanns keep the case alive publically and why Scotland Yard don't seem to suspect them in any way is truly baffling though.
Ultimately, there is not enough evidence to proceed with this case.