I await someone who has run every marathon in the world to give the definitive answer to this. Until then it's Milton Keynes all the way.
I see a flaw in your thinking.
The person who has run them all may well give a fairer view than the person who has, say, only run Milton Keynes. But, it's just one person. Do we really trust their judgement that implicitly? I think what we have to wait for here is for all of the people in the world to have run all of the marathons in the world first. Only then will we get the cross-section of opinion that we need here.
Having said all of that, i'm still fairly certain it will be Milton Keynes.