So A Emoji is the replacement for the possibility to explain why you plus or minus repped a Comment, I think this is much worse than to explain the person why you disagree and to do this with a PM is a lot worse than to do it with the rep posting as most will not make a PM to explain why they disagreed with your post. People are lazy and after you minus repped someone why should you then go to open a PM discussion with him to explain the neg rep you gave?
The primary purpose of any forum is to facilitate civil and open discussions between members.
If you disagree with someone's post, then you should post a reply in the thread explaining your viewpoint to the poster and other readers, and thereby move the discussion forward.
The private, one-way reputation comment system encouraged lots of negativity and members taking "pot shots" at one another, and resulted in a constant escalation of "revenge reps", as well as coordinated "neg rep" campaigns by one group or society versus another. For whatever reason, the semi-private nature of reputation comments seemed to encourage a drastic increase in toxicity and abuse between members.
None of this was productive or useful for anyone involved, not to mention the hundreds of hours of time wasted by the forum staff dealing with reports of inappropriate reputation comments.
My view is that the new reactions system is a good way for members to quickly show their appreciation or feelings for a thread or post when they don't have time to post a full reply, without all of the drawbacks that the old reputation comment system created.