First, before the criticism: the content here is still excellent, and you guys are always admirably aware enough to address things like this when they happen, and I appreciate that.
But that said, I have to echo everything @samdiener has said. You mention that you've seen commenting activity go down, but that has to be playing down how little people interact anymore. Since the switch, there have been exactly 13 posts on UW that have 10 or more replies. When there are comments - which is rare - there are generally fewer, and/or one thread of conversation as opposed to the many that used to develop.
Reddit has become your comments section, whereas before we used to have two separate but vital discussions taking place. A recent Ultiworld Disc Golf article about the Williams suspension had 52 comments on Reddit, and 0 on your native site. That's part of the deal with aggregation sites, but I'm pretty confident that if there was a comment system more readily accessible here you would see at least some of that staying on-site like it did with the previous system.
The most common feedback has been for a same-page reply function, but that has been refuted philosophically by the developers and no third party has written a plugin. I can appreciate a philosophical stance and the Discourse devs are certainly entitled to theirs, but why hitch your wagon to it then? There is a year's worth of decreasing participation significant enough to warrant an explainer article, so you're definitely aware of it. At this point,
I'm also willing to admit I'm doing it wrong, and I'm happy to try it again with some of the new info I gathered here. Along those lines, are there any examples of the Discourse system being used successfully elsewhere? I'm curious to see what I'm missing.