CSS wizards can probably suggest tweaks to the existing styles to make 'em more modern. I'm not enough of a CSS guru nor "modern" to know, though. :) The look hasn't bothered me and nobody's submitted a patch to improve things, so alas. As always, patches are more than welcome (but as a volunteer I cannot guarantee that they would definitely be tested/reviewed in a given time, or merged)!
Comments is one of those social tools extensions which doesn't even require SocialProfile and it's a pretty popular, basic functionality, so I'd expect plenty of sites out there to use it. (If only WikiApiary was a bit more stable...) Here's an example page on Brickipedia, the LEGO encyclopedia hosted by ShoutWiki, which uses comments.
Ah, ArticleComments...I remember that. It's been a while, eh? Out of sheer curiosity I did some digging, dug up the MW 1.20-compatible version and tried getting it working. It wasn't even that difficult, although it's still not working perfectly for me locally. The code somewhat shows its age, although admittedly its brilliance is that the "comments" are indeed just regular wiki edits on a regular wiki page. For example, the PostComment extension by wikiHow took a similar approach.
Flow was always dead-on-arrival software, but the problem was that you couldn't say it out loud that the Emperor has no clothes. I'm sorry you ended up wasting your time with it. The WMF has a rather poor track record with discussion-related extensions, although Extension:DiscussionTools is doing better than Flow ever did and it has been more positively received by the various communities on WMF web properties.
Migrations absolutely are horrible to do, and it's oftentimes just uncharted territory, and basically always so with MediaWiki extensions (e.g. "how do I migrate from extension X to Y or Z?"). There are various reasons as to why, but I think the main ones are technical complexity and a ridiculously small target audience, plus probably funding or the lack of thereof.
Predicting the future is, of course, impossible. There are many reasons why some of the social tools are kinda horrible, as I explained in my earlier response; and yet, bizarrely enough, these same reasons might also be why they're surprisingly great (in my biased opinion, of course). Comments and others precede ContentHandler by several years, and while this has rather obvious drawbacks, it also means that these extensions have stayed surprisingly stable over the years (or decades, I should say, for a lot of them will be turning 20 years old in ~2-3 years (!)) by not relying on the standard MediaWiki way to do things. Whether this is or isn't something you want is a question only you (and your community) can answer.
Also, I should point out that there are probably some other, likely even better commenting/discussion-related extensions. I just happen to be most familiar with the extension that I maintain.