Can’t you delete the automated tags? They appear for me when I write a post, too, but I just delete them and add my own. I don’t see automated tags when I write a response to something, though.
What browser are you using? I’m using Chrome and when you click through to an article you can see the number of responses in the ‘footer widget’ that appears at the bottom of the screen. You can click that icon to jump down to the responses faster. (But perhaps it may be better to instead highlight text and respond to specific things anyway? That’s more the ‘Medium way’ because it builds interest into the article itself.
As mentioned, Medium is going through an evolution right now, having only announced the changes that compelled my to join in April. I have faith they’ll iron our the kinks and things will improve all round, in time. The main thing is that its a nicer and easier thing to use (for me anyway), as both a reader and writer.