What recommends this arrangement over any other arrangement?

Nothing at all, except that it shows there exists such a correspondence -- which is the only question of interest when talking about the "size" (cardinality) of sets.

(EDIT: Perhaps I should add that this question of existence is interesting because the situation can be quite different for different pairs of sets: while there exists a 1-1 correspondence between primes and natural numbers, there does not exist any such correspondence between primes and real numbers. In that case, all mappings will leave out some real numbers -- or duplicate some primes, if you're going the other way.)

All the other ways of "counting" that you're thinking of are just as "valid" as mathematical ideas, for whatever other purposes they may be used for. Here's an example, actually: the fact that you can think of a way of making primes correspond in a one-to-one fashion to a proper subset of the natural numbers (not including all natural numbers) succeeds in showing that the set of primes is no larger than the set of natural numbers.