I consider the exclusion of wordpress core files a bonus. I have tons of core code laying around.. and I usually go get a fresh copy of the core from the repository anyways.
I remember on the joomla sites I used to use akabee (or whatever it was called.. and it was pretty slick.. but a ton more stuff to configure because it didn’t know how to exclude basic stuff). It’s backup files were way more bloated than they needed to be (unless I spent hours configuring it to the ‘T’).
This is so much more the breeze to use. I think this is an unfair criticism. If you have a highly customized core, then I repectfully submit that your approach to wordpress development is questionable..
All customization should be happening in the Themes and Plugin directories.. so.. that is what gets backed up.. along with the database and uploads. Perfect, IMHO.