I can definitely understand the confusion; when I was a newbie here almost 3 years ago, it took me a few weeks before I realized how to reply to a root node. (For somet reason, my eyes kept drifting over the blue bar because I thought it was simply a page divider, and it also didn't occur to me at first that "Comment on this Node" really meant "Reply to this Node".)

So yeah, I can definitely see a reason to change it; of course, I'm used to it now, so my opinion is largely indifferent. :)