I've run a gaming community with a general "Mess hall" forum for ~12-14 years now, and Engadget is making the same mistake I did a few times: expecting too much from their discussions.
From the article:
because so many of the replies are hateful
That's a matter of moderator opinion. I've seen overly sensitive moderators consider any strong opinion "hateful" merely because they disagree with it, or because it has the word "hate" in it. I hate politicians that try and push for backdoors into encryption, but it's really childish if a moderator would want to censor such an opinion.
Articles that mention Apple deteriorate into arguments of iOS vs Android
So what? Again, it's moderator opinion that such debates don't add value. Nested comments help isolate these debates to as single thread.
replete with grade-school name calling
So what?
At the end of the day, Engadget has failed to understand that comments are a form of content in and of themselves, and a draw for traffic in and of themselves (like on Reddit and HN). Sometimes they add meaningful points and counter points, sometimes they're hilarious, sometimes they carry strong opinion, sometimes they carry questionable logic, and sometimes they're flat out mean or stupid. That's how things go. You simply accept the bad that comes with the good, try not to play God when it comes to deciding which comments are valuable and which aren't, and moderate the really bad stuff.
Where you run into problems is when you get YouTube quality comments - the kind where spelling, grammar, punctuation, and any semblance of structure or intelligence is absent.