I agree that there are some quirks to music theory but ultimately I think it's a very good system that was been refined over hundreds of years.

As for your point about A->B being a larger interval than B->C. There are two half-steps in the white keys (B->C and E->F) because there are two half steps in the major scale! This way, you can play C to C with all white keys and get a major scale.

A major scale is probably one of the most fundamental building blocks in western music theory and it's encoded right onto the keyboard layout itself.

The oddities of music theory are no more strange than all of the strange things in the English language that we just shrug about and move on once we learn it.