Was online discussion better when blogs were in their heyday? I don’t think I have rose-colored spectacles, but it seems to me there was at least more room for productive discussion. There was a greater chance that a commenter had been following your blog for a while and knew where you were coming from — and similarly, there was a tendency for a community of commenters to develop.
Now it seems like commenting culture is like guerilla warfare — people swoop in, take potshots with no context whatsoever, and don’t even stick around for the responses. No one responds directly to what a particular person is saying, but only to the kind of thing they think that kind of person says. Plus there’s the weaponization of comment through orchestrated harassment campaigns.
There are still people trying to have a genuine dialogue, but it’s hard to filter out the noise. It was never great, of course, but now it’s even worse.
An und für sich 
I don’t know, this is kind of weird to me since I am not on Tweeter and only look at blogs, and there still seem to be plenty of them, and discussion forums, which people also say are on the way out but still seem to be around. I don’t see the appeal of that other stuff.
I think it is an instance of a wider phenomenon of internet community growth. At first a blog/ forum/ &c starts out with a group of people with similar interests and skills. More people join as the content is high quality. Then, as many people get involved, the quality drops because the new folks aren’t as involved or educated in the subject matter as the founders, increasing the noise. Also, with growth, we get people that have agendas of their own trying to hijack that community. As noted by OP, strategic trolling© has now basically become a paid profession.
I’ve seen complementary complaints (on other blogs) that all the discussion has moved to ‘walled gardens’ like Facebook, which insulates the group. The trolls are blocked, but no outside thought enters either, leading to an echo-chamber and stagnation.
Until someone figures out a happy medium, this split is the best we have at the moment.
Perhaps in the early days, blogging was a contingent extension of other formats and the norms that govern them. Overtime it has grown its own autonomy, which has exacerbated possibilities which are already present when one tries to communicate.
The physical absence of author, combined with the ease of opportunity to interact in the medium removes checks on behaviour. When you are commenting on a blog, it is easy to forget that it is the semi-personal/public space and regress into narcissistic shadow boxing.
Authors should also bear some of the responsibility, but there is a trade off between protecting your writing from a particular reading, and pay off for the reader.
The answer depends a bit on what you mean by their “heyday”. I suspect that, as a group, the early adopters of blogging and commenting had a different temperament than the general population that joined later, so that might have influenced the atmosphere of the blogging ecosystem in the early 00’s.
Personally, I do think that the quality of conversations on social media is worse, with twitter being the worst of all. A few months ago I was stuck at home sick, and out of extreme boredom I started browsing the archives of the Theory’s Empire book event at The Valve (11 years ago already!). I couldn’t help thinking about what a massive train wreck it would likely have turned into if twitter had been around at the time.