I not a big fan of the comment system either, but it seems like SmarterTools is against removing it. Obviously, Tim must love that design... And employees generally don't argue with the CEO, unless it's me, I'm not afraid to say something isn't working.
But, maybe there is a compromise, have both systems and allow the user to select which display format they like better. Linear or Comment System...
Under the Linear systems, all replys/comments are displayed in a chronological order and look like normal replies, They can even add in the header of the reply (This is in reply to post #14), so you can tell which reply it was in reference to.
Then instead of a "post comment" box, there will just be a reply link, that will just append to the "Reply in Thread" on top someplace that says "In Reply to post #14". Each post in a thread will then have a label with a #, which will also be useful cause then you can link to that specific post with an Href.
Where the #14 will take you to the 14th post in that thread.
Then it's a win/win for everyone..