I am really flummoxed by all this, I know we don't have anything like the whole story but none of it makes any kind of sense.
The one vital thing missing (in my view) is the lack of any creditable motive - by anyone at all.
The first speculative theory of an opportunistic abduction seems to have lost ground to the extraordinary man Er... childhunt that has been ongoing for some four months - surely that would have tested the nerve of any but the most determined abductor, unless Maddie had already been killed, short of an accident or wild sex attack why would anyone want to abduct and kill her in a strange place?
Kidnapping must also be discounted by virtue of no ransom demands - unless all the publicity frightened them enough to kill her and move on.
Accidental or otherwise homicide doesn't really ring true either seeing as they are doctors, Shipman certainly knew how to cover up murders so I'm sure the McCann's would have the same skills. Even so what was the motive? And why there? It is so much easier to lose kids in crowded places. Sedation to keep them quiet maybe? again, they are doctors if they don't know how to administer a sedative then god help all the rest of us.
Maybe they really hated Maddie. Perhaps she got on their nerves to the point of killing her but... Wouldn't they have disposed of the body before raising the hue and cry and not risk hiding a body for three weeks while everyone in the world is looking for her, the DNA in the car defies logic or was an staggering risk taken in desperation. Why? people had all but stopped searching the near area by then.
There is an angle that no-one seems to have thought of yet, and that would be a personal vendetta by someone with a grudge manufacturing a scenario that must keep them twisting on the horns if not ultimately convicting them.
There are people evil enough to want that kind of revenge for something, and a Doctor and a Surgeon must have quite a few deaths through their hands. There was the "They've taken her." cry after all.
I believe there is quite a bit of milage left in this saga.