I think a lot of the problem comes down to all of the siloed walls out there which are causing most of the friction. We're still relatively early days yet and only a tiny few are using the concept of salmention which would help keep running threads working properly. Admittedly having the context live somewhere and then having proper threaded communications isn't easy, so many do what they're able to for the moment.
I'm usually attempting to manually accomplish salmention as best as I'm able, but I may not hit every syndicated target unless you're displaying it directly. Additionally some targets just don't make sense--I'll webmention your original, for example, but this lengthy reply just won't look right at micro.blog if you syndicated a simple headline and URL there, so why bother since you'll see it at the original anyway? Others who are on micro.blog may miss out on part of the conversation, but presumably if they're looking at your copy on micro.blog, they'll be able to see the original as it was intended.
Colin, you mention that not all of your content needs to go to micro.blog. Perhaps, but to think so in my mind is part of the older silo way of thinking. The only reason you're syndicating there is as a stopgap to reach the people who don't currently have the time or luxury to be doing things the way you are. Otherwise they could subscribe to you directly at the source (and potentially even circumscribe the types of posts, keywords, or content to get exactly what they want from your site.) In some sense you syndicate there to reach and communicate with the non-IndieWeb crowd. Perhaps some of your content doesn't make as much sense there as Micro.blog is limited in what it is able to do, but that is its limitation, not yours. Eventually in a fully IndieWeb-ified world, everyone would have their own domain, their own data, and syndication of any sort won't have a real need to exist at all.
As to Jack's comment, syndicating things out to multiple places is often difficult as is getting all the responses back. (Fortunately services like Brid.gy make things far easier though they don't cover all the bases.) I do it in large part because while I prefer to own all of my content and have all the conversation take place on my personal site, I can't necessarily make that choice for everyone else. My mom is likely to never have her own domain much less a site. The only way she'll see my content (whether it's meant for her or not) is to syndicate it to Facebook. For those who aren't yet aware of the IndieWeb or using it, they're still reading and interacting on other platforms, which, for me is fine since I can still have my cake and eat it too. Eventually there will be inexpensive platforms that will let people who don't want to deal with the development cost and overhead that allow much of the IndieWeb-types of functionalities they're not currently getting from their silo platforms for free. I suspect that these will be easier and easier (as well as cheaper) to use over time. I suspect more people will use them for their freedom, flexibility, and increased control. Until then, I have the privilege of using my site much the way I would Facebook, Twitter, Instagram, Google+, Flickr, GoodReads, etc., etc., I just get to do it through a more unified experience instead of having to juggle dozens of accounts and only being able to interact with my fractions of friends, family, and colleagues who coincidentally happen to be spending the time and effort to interact on those websites. As an example, I have dozens of friends who interact with me on Facebook about things I'm currently reading or finished reading, but if I was only doing this on GoodReads, they'd never have a chance to see it as they don't have accounts there or even know it exists. (Coincidentally, this is also the reason that GoodReads and most other silos allow one to syndicate their accounts to Twitter, Facebook, etc.)
Not all social sites are as lucky as Facebook to have such massive adoption. This creates a value imbalance with respect to the classic "network effect" (see: https://en.wikipedia.org/wiki/Network_effect). Philosophically I think that an decentralized and distributed version of IndieWeb philosophies add far more value than having hundreds or even thousands of individual silos.
Invariably some people are likely to stick with Twitter, Facebook, or others because they don't have the same values I do. (Currently I suspect the majority do it because it's frictionless and easy.) But this doesn't change the fact that one can't have a "universal" conversation if one prefers. When I look at various platforms, some of them have different personalities and types of conversations because of the (possibly) self-selecting group of people on them. I loved Twitter more in the early days because of it's smaller and more engaged community--things have naturally changed drastically since those early days. Micro.blog is a bit more like it now, but to me it's not so much a social media replacement for Twitter. To me it's really a social reader that I use to quickly follow a subset of interesting and thoughtful people until I have a better social reader built into my own site. The conversation would be somewhat different if these silos were working on niche audience content like knitting or quantum mechanics, but typically they're not. Most social silos are geared toward mass adoption and broad topic discussion or content posting for everyone/everywhere. Their goal is for their site to be the proverbial "phone number and dial-tone of the web". Why do this when I already have a connection and a "phone number" that is my own site URL?
Jack, while some bloggers have turned off comments, they've often done so saying "Post your reply on your own site, or on Twitter, Facebook, etc." This has just pushed the conversation on their ideas off somewhere else which is disconnected and not as easily searchable or discoverable. And without some kind of notification mechanism, the author of the original post has no idea it exists. (I'll elide a conversation about blocking trolls and abuse here.) I've written some thoughts on comments sections in reply to such a blogger who recently re-enabled comments which also links to several interesting articles about the pros/cons of having comments at all. To me, between webmentions, spam filtering, and even moderation, we're lightyears ahead of where we were in the early 2000s.
One other thing I do find interesting is that the way all of this is set up is allowing us the ability to write extended thoughts and extended multiple replies (with civility as relative strangers). I don't think there are many sites on the web that allow this type of interaction, and they certainly don't do it with anything remotely close to the open architecture we're using. While at times it can be a headache for maintenance and problems, I find far more value in it than using anything else.