Alright, so I think I have finally figured out how to best communicate what I did not like about this game. And I think I can explain that easily using Chapter 21 as an example.
I see what you are saying; but really how long did the chapter take? 10 minutes at most? This isn't some 30 minute or hour long fetch quest bumping up an open world games playtime. To me that's a perfect amount of buffer between an intense fight and another intense section. It also gave Nate a chance to reflect on what has happened so far and you can hear him say some of it out loud. Also provided some really cool visuals. I actually loved that chapter as it gave me time to think about the story as well. It's probably a really poor chapter on subsequent play throughs but I'm willing to bet they tailored the game to the majority of people that will play it through once and be done.
It's perfectly fine to call it filler, I'd argue just the opposite. But I'm also surprised that you hate it so much that it's really harming your experience so much as to warrant very long posts discussing it. Most have a problem with the pacing, but it's a minor knock, seems it has borderline caused you some heartache.