I agree, and I don't have that many files where I have chapters.
However, on my remote, I have discreet next/prev Track buttons, and my wife uses these to skip forward/back through tracks. And, I have (what I'll call) Fast-Forward/Rewind buttons (the arrows without the line) which are programmed as 30-ahead/10-back buttons.
I've, in the past, told her that to navigate chapters (on the few files where we have them) you just use the arrows instead of these, and that works. Usually she doesn't care about going to a particular chapter. It is a way to "fast forward" faster than the typical 30-ahead/10-back.
But... This isn't used frequently at all in my house. I do wonder about people who actually use MC to play optical discs, though, as the expected behavior there would be to skip through chapters (that is the standard behavior of a DVD/BluRay remote control, when you use the >>| buttons).
I don't know. I don't have strong feelings, but it brings up a vague disquiet. Like I said, it is more consistent, which is usually good. But in this case, it is really "burying" a fairly important (to some people, I image) function under a menu. And, to work around it, you'd really need a remote with 3 sets of discreet FF/RW buttons: one for "true" FF/RW or x second skipping, one for Track Forward/Back (the arrows), and one for ONLY chapters.