The notion of a 'Flagship' is ridiculous and is the problem when we look for something to be everything for everyone when we all want something different albeit slightly. Why not ask the question what is the Flagship lens, as each of our requirements are different we are likely to disagree. Can anyone tell me what BMW's flagship is, or Mercedes, Porsche, we may well all have our own idea's. Perhaps a better way to view it would be to say, 'Which of canons camera's leads the way with cutting edge technology and how does it compete with the competition'.
It seems to me that we spend way too much time being critical when a newly released camera doesn't meet our individual needs. It seems to me that Canon made the first steps towards improving low light resolution with their recent camera's 1DX, 5D3, something that people had been critical of for some years. This is a journey and not everything will be resolved in one camera.
So if we are to have a flagship, then for me its the 5D3 as it meets my requirements at this time.