I always suspected the parents from day one, it reminds me of that JonBenet Ramsay case from 1996.
My theory: her parents, or at least one of them, is/are responsible although I do not know why and I do not know exactly what happened.
The McCanns take a tour of Europe and the world etc. to "raise awareness" and stayed in Portugal to "look for their daughter". Their whole attitude since it happened has been extremely fishy and some things do not seem right at all, things are not adding up.
The reason they went off travelling and stayed in Portugal as well instead of going back to the UK was because they did it, and the UK Social Services and UK Police Services are far more efficient and ruthless, and would suss them in about five minutes. Game over, welcome to prison. I think they are as guilty as sin and are trying to postpone the inevitable, but we shall see how things pan out as the questioning and investigation continues.
Stay in Portugal where the big guns in the UK cannot get you, whipping up an international media circus at the same time to draw attention to yourselves.
Part of me hopes it was the parents, the authorities prove it and a lid is put on all of this. If her parents were responsible and she is indeed dead then these people have conned the entire globe.