I think the primary problem with the game's ending, or at least, the thing that seems to be causing the biggest schism, is that the game wants you to care about the kid & his dad, but that endeavor is completely handicapped in how the information about those two is relayed. Even in its more touching moments, it's always of secondary (sometimes tertiary) importance to Henry and Dee's back & forth.
It never rises above "a thing Dee talks about when she's not talking about you, or you and her, and/or her." Her feelings of regret for leaving him out there come far too late, and never pack any real punch in comparison to the potential relationship between her and Henry (real or imagined), or the conspiracy that starts to unfold, which only seems interesting when dialog options ask you to lean into the idea this is some Twin Peaks-ish mindgame fuckery.
That said, when the credits roll and you see the snapshots of the kid and the dad, it works like it should have been working all game long. But unfortunately, the game's already over at that point.
It's a tough one, because part of the reason the game works so well as it does is the interplay between Dee & Henry, but in order to make the game have the oomph it really, really wants, you have to minimize that interplay and push more focus on the story of the kid & the dad, and make that a much more focal part of the mystery right up front. They didn't do that at all, and so you have a game that feels more or less like an Alex Garland screenplay: The first 2/3rds are delivering splendidly, and then when its time to actually deliver on the thesis, the rails get jumped and we just sorta rush towards that endpoint whether or not its earned, or even tracks with what came before.
But then again, I really like 28 Days Later, and Sunshine, and Ex Machina. And I like this, too. I'm apparently okay with jumping the rails with the story.
I just finished the game about an hour ago, and I'm still processing the whole thing, but something about your (nicely put, btw) criticism here stuck out to me: The notion that "Ned and Brian's story wasn't in the forefront, so the ending and overall effect doesn't work" only really applies if players are only willing to play through the game once, never go back, and generally assume the game has one singular "point" it's trying to make. The game has a lot of misdirects, but I don't think making the game more about Ned is really necessary: by having the Ned sections only doled out in small spots, it's something that I actually find more compelling because I have to go back and stretch a bit to recall and stitch together what happened.
Finishing Firewatch instantly reminded me of two things, both of which I know that Chris Remo, Sean Vanaman and Jake Rodkin are fans of: Thirty Flights of Loving, and Sleep No More. (Well, three, I guess: Gone Home is the obvious connection.) Tonally, both Thirty and Sleep No More are pretty different from each other, but both are all about not having any living clue what the fuck happened at first blush, then looping through it several times to piece together the story. Finding things that you didn't think were important the first time and then considering how they work together.
I actually like how Ned's story is punctuated in several isolated spots, and how I had no idea that he'd actually be a factor in the story at all. And while I understand how a lot of people could see this as a flaw, in the more classical understanding of game design of "foreground and spotlight Things of Great Importance," I feel like I've listened to enough commentary from the Idle Thumbs crew to know that they'd probably hate making such obvious overtures. Chekhov's Gun and all that.
It wasn't until the very end, when Delilah is pissed off at Ned (and my Henry choices were actually defending Ned a little), that I realized how all three of them were the same: when Dee says "how the fuck could Ned have not reported his son's death, even though he knew he should have done the right thing?" I knew the game was gesturing at how Delilah and Henry did the same thing. Dee says that she drifts from Javier because she just never bothered to come home after that death in his family; she knew she should have, but she just ... didn't, in that evasive, human way we all occasionally default on what we know are the good, right, moral ways of living. Just like she doesn't report the hikers, though you could easily say she's trying to protect Henry (but who knows? Could just as easily been all about avoiding her responsibility. She constantly talked about getting drunk, sitting alone in the woods, and just not having to deal with anything).
Similarly, I ended up having Henry say "I shouldn't be here" whenever I could, because it was true: he shouldn't have been. He should have been the Good Husband, beside his ailing wife, but being the Good Guy (or the Good Girlfriend or the Good Father or the Good Citizen) can be just so fucking exhausting sometimes, right? Either you get tired of it and just give up or you have a momentary lapse and then you're so wracked with guilt that you can't even bring yourself to think about how to fix it, so you just ignore, evade, escape, run.
My initial gut-check on Firewatch is that it's about that ugly human instinct to Not Want To Deal. Faced with a painful truth, the brain can go through pretty contorted mental gymnastics to avoid having to deal with it. It's interesting that Delilah is the one to break character and just flat-out slap Henry with the cold truth: Go be with your horribly sick wife, Hank. I felt myself super disappointed that Delilah wasn't in the tower when I got there, and then I hated myself for feeling disappointed, because the whole "relationship" (which even Delilah questions and feels awkward about questioning or even bringing up) is a figment. It's Schroedinger's Cat: it exists and doesn't exist, and as long as you don't directly talk about it or acknowledge it it can be both of those things at once, so can't we just lie to ourselves and just let things be and enjoy a snarky chat together? That's why Delilah can never be there for Henry - that would be the super sappy, shitty Hollywood ending that accomplishes nothing.
...Sorry, this is long and rambly. I'm exhausted and not making sense, but felt like jotting down some reactions before I went to bed. Finishing Firewatch left me a fair bit deflated and disappointed, but rather than this being a criticism, I'm more interested in trying to figure out why I was disappointed. That's something games almost never do, but it's something that can be employed to honest, gut-punching effect in literature and film.
TL;DR: Forget it, Henry, it's Chinatown.