I would say a big disadvantage of doing it this way is you're serving up different CSS/JS files for each page.

You don't have to, though. You can put everything into a single global css file, and be done with it.

And I haven't implemented it, but I can immediately see easy ways to package it all up into single files that can be easily cached.

It's easier to consolidate the files programmatically after they've been logically separated, than to logically separate out of a monolithic location.