Not really addressing the concerns they seem to be dealing with in the article, but "embedded comment threads" was my favourite thing about Google Wave - you co

Not really addressing the concerns they seem to be dealing with in the article, but "embedded comment threads" was my favourite thing about Google Wave - you could embed a thread anywhere (like, one wave for each blog post) and see/reply followups directly from your mail client (well, wave client). That way you weren't making little "data islands" all around the internet (that you're not likely to get back to) and there was more chance that a given idea/topic would be more thoroughly discussed. In theory!