Well most all users don't use threaded mode.
Myself included.
Exactly; not only do I not use Threaded mode, there are several issues (such as replies not linking as a child to items you may be replying to if using the Quick Reply box) that make things kind of "wonky".
Basically, if you plan to use Threaded Mode, don't use the Quick Reply box (which IMHO is one of the more popular features that Rick got from ubbdev over the years).
I can also state that I don't know a single forum that still uses Threaded Mode; which is funny since several competing products have removed the option completely and that's one thing that made Threads a big deal (you'll find a lot of users who converted to threads from Classic just demanded the classic features ported up (myself included) and never really got onboard with the whole threaded mode thing).