I wish Slack had a notion of Threadmaster(s) on a channel who could drag other people's messages into and out of threads. Because with people who aren't familiar with Slack or aren't committed to threading, you end up with a split brain between the conversation in the thread and the conversation at the top level. I get that it's hard from a permissioning perspective since anyone can create a public channel, but this should be a solvable problem.
They fixed your second problem with the thread tab, which shows all threads you are part of. I find that pretty convenient since it sorts threads by the latest message added, not sorted chronologically by the first message like it is in the normal view.
I also think it's problematic (and, granted this might be more on users than slack) - that a thread off an @here comment pings everyone in existence on every reply. Maybe I just wish our admins would turn off @here for general usage though ;P
I don't like that you can't come back later, select a bunch of messages or threads and say "Group into a thread" to clean up people not using threads.
Also I kind of hate when it's a week later and someone responds to a thread and you get pinged, but can't find where you got pinged from without clicking the dynamic group to see all thread activity.
Also, it really annoys me that threads open on the right with the text entry on the lower right when toast notifications on Windows pop up on the lower right, too. Great, now whenever someone replies I get a toast popup blocking me from seeing what I'm typing. Thanks, guys. Sure, that only happens on one monitor, but that's also the same monitor that I want my toast notifications and my Slack to be on because it's where I'm often looking.