If two people enter into an obstacle race, you don't expect one of them who is losing suddenly insist that it should have been a flat race without any obstacles, and that they should be awarded the victory on that basis.
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Primary systems and general elections are different animals, and they have different purposes.

The point of a primary system is presumably to ensure that the best candidate wins through to stand in the election. Its not an election in itself, its a preparation for the election. It is at least arguable that primaries are a better way of ensuring that the best candidate is put forward.

When it comes to the election it is not about ensuring that the best candidate wins, but the one who gets the most votes. That applies even even if they are not the best candidate.