Nested replies are definitely better as a way of consuming a post and its comments once and then never thinking about it again. For an asynchronous discussion between several people they get unwieldy after a few rounds of replying. They also make it harder to coherently reference points made cross-tree. That plus algorithmic ranking gives a constant feeling of "gotta refresh to see if there's new stuff" that serves a site like Reddit well, but it makes it much harder to have a longer discussion with more back and forth.
Having recently started participating in a community where most useful discussions are on a PhpBB forum, going back to linear posting was actually refreshing. It's easy to stay on top of because you can check in once a day or so and see just the conversations that have updates since you've last checked them. Threads being sorted by most recently updated means you focus on where there's active discussion. And once you've read those things there's no reason to stick around. "That's it! Get back to doing something useful."
Obviously, this doesn't really scale to a community the size of reddit, but I think it's really pleasant for medium-sized communities.
I think you can mostly solve these problems by changing how the trees are sorted rather than eliminating them entirely.
Here's the usability problem: You're 40 pages deep in a 100 page discussion and you see someone asked a question that you also want to know the answer to. How do you weed through the comments in the remaining 60 pages to find only answers to this question and relevant tangents? I've yet to see a conventional forum come up with a solution that doesn't involve a lot of friction or potential for missed information.
It is far too common for a forum's built in search tool to fail me for some reason or another, leading me to manually scan the entire thread. I may be willing to do that work if the information I am seeking is very important, but will I still feel that way if I just have a hunch that maybe I can provide my own input for someone else?
An upside of linear threads is synchrony, you've pointed out. But the linear thread format isn't incompatible with nesting necessarily, with quoting you're effectively having soft-nested conversations. What's lacking is UX that emphasizes this mixed threading style, and thus benefits from the best of both.
It might surprise you that, I think 4chan explores mixed threading like no other website does. Threads are linear, but quoting results in backlinks meaning isolated conversations are easily navigable, filtering out the "firehose". There's also a button that looks like [-] that can hide a post and all its nested replies, this can hide a specific reply chain from the linear view of the thread. I gave the system a bigger eulogy over here: https://news.ycombinator.com/item?id=33567593
Having recently started participating in a community where most useful discussions are on a PhpBB forum, going back to linear posting was actually refreshing. It's easy to stay on top of because you can check in once a day or so and see just the conversations that have updates since you've last checked them. Threads being sorted by most recently updated means you focus on where there's active discussion. And once you've read those things there's no reason to stick around. "That's it! Get back to doing something useful."
Obviously, this doesn't really scale to a community the size of reddit, but I think it's really pleasant for medium-sized communities.