I'm on a couple slacks, some where local culture is firmly built on threading, and some where it's not, and the former is at least 10x more productive and enjoyable. If other members of the community had the option to view things threadlessly, they would start replying to threads in the main channel, and ruin the experience for everyone else.
You might say this wouldn't happen much, but think about how hard it is just to get your coworkers to stop using @here frivolously.
However, if so many of your users are complaining about something, and if the complaint is about something as important as “losing messages,” then something should be done about it. It’s no longer enough to say that “but it works for some people” or to say that “options add complexity.”
Our entire core team has discussed this. Nobody wants threads. They all lose messages due to this. But sometimes we accidentally respond to messages that start a thread. So, we want this option to be removed for the entire organization. But we can’t.
It’s an option that’ll have cost, yes. But, it’ll be much simpler than many other complicated (and low value) things Slack has worked on in past two years. Those other things are also adding complexity, slowing down dev, increasing things to test, etc. And, again, this option solves a serious and fundamental problem of losing messages. So, it’s worth the cost for many of their users.
Are you familiar with the way you can cc: the channel on a thread comment when you’re concerned people might miss it?
Vocal minorities shouldn't drive product decisions.
This is obviously a hard problem to solve without just making it back into email. Muting apps that spam notifications for someone else’s benefit would be a great start. Not allowing bots to spam new threads at you and cleaning up old threads automatically would also be great—having a ton of old threads brings the client to its knees on my dual core laptop.
Slack just sucks for anything you need to find again, IMHO, it should be treated like it's ephemeral. The logs are worth keeping as leverage against employees of course.