Q: Why are my pads worn at a diagonal?

A: Cause that is the way Yamaha made them. 

But only God know why they thought it was a good idea.

Brake pad break-in 101
http://viragotechforum.com/kb.php?mode=article&k=94

Brake Fluid Facts
http://viragotechforum.com/kb.php?mode=article&k=29

This is a set of new brake pads.
[I do not like this pad design they are almost gone new.]

Bad XV750 Brake Pads

Similar to auto / truck brake pads there is a bit of raised metal just above the min wear of the pads.
That is so you hear that annoying brake bad sing or high pitched noise and know they are almost gone.
Though that noise is not 100% accurate, but check anyways.
On most car/truck pads its an extra metal tab that clips on so it can fall off n such so don't depend on that noise either.