If there's a Theory of Everything then surely all physical existence can be expressed with mathematics.

In Europe at least maths can't be patented but applications of maths often can, just like software can't be patented as such but if it has real-world technical effect it can.

A new rocket launch trajectory may be "just maths" but if it reduces fuel consumption then it arguably isn't "just maths" and so will probably gain a patent.

This approach seems compatible with the quid pro quo intention of patents.