This is one reason QM is not exactly an "elegant" theory (imo). QM can pretty much be thought of as a bunch of rules invented by people so that the answers come out correctly. When Planck invented his constant (h), he had no idea why it should exist, he just noticed that by quantizing the allowed energy levels in a black body, he could resolve the ultraviolet catastrophe. When Schroedinger came up with his equation, he had no idea what the wave-function was! He though it was some electron cloud density distribution and only later did Born come up with his probabilistic take on it. Schroedinger himself never accepted Born's postulate. So, in this sense, there is no good reason exactly why the wave-function absolute squared IS the probability distribution, but it's just that the rules and math work out that way.
This is NOT to say, though, that QM is somehow inferior. It is a VERY powerful tool that we have, and is one of the most physically accurate ones.