There seems to be a limit on the number of reply buttons per thread. Sometimes after someone's reply there is a "message" button or a "reply" button. Sometimes there is nothing, Why?

It indents a little more with every reply. If it can keep indenting more, the text will eventually become totally illegible and squished. So, there has to be a limit on replies. You can always go up to the last comment that has a reply button and leave one there. The redesign isn't set up this way, BTW.

As for the message option, it provides it when you're friends with the person. 

Hello Just Asking. I did like that aspect of answerbag better. Have you considered doing it that way with unlimited replies? Or perhaps indent the first comment under an answer and just indent the rest the same as the first but all but the original answer indented? I mean don't indent any of the answers but indent all of the comments.