There are some improvements to be made yes, but for me, the only thing I have a problem with is when my reply feed is filled with persistent replies from the same person who I haven't replied to. My solution to this is to tell the person they have been muted, and once they know, any replies they leave in my reply box will be flagged.

Your reputation is higher than the trolls. So retaliation flags won't affect your reputation. Just don't go flagging everything of theirs to start a flag war. Only flag the replies that you see appear in your replies feed AFTER you have muted the troll and they are aware you no longer want to partake in a debate/troll fight! - which they should already be aware of from what I've seen.