I do understand that the current web infrastructure is not made for this, but given demand, it /could/ be adapted for the sort of reading that we are nostalgic about. There are obscure forums that I sometimes read on the portal bsh.co.il - this is an Israeli social work portal. Click on a message in a forum like
http://www.bsh.co.il/forums/AllMessages2.asp?Fnumber=10 - there is going to be a checkmark next to the message you clicked from now on, even if you reload the browser (presumably, there is a cookie). This is a small custom-written forum with very little programmer muscle behind it, I doubt it's more than a couple of guys. If they can do it, everyone can do it - and it's a small step to hiding threads completely, etc., etc.
I've concluded that there is just no demand for sophisticated threading/reading software of the type we had in the '90s. If there was demand, there is certainly technology to fill it. If they can run Linux in a browser complete with a little C compiler, they can run the equivalent of trn. As you pointed out yourself, Gmail covers the basics already - why not make it more sophisticated and bring the technology to Google Groups? No demand. Otherwise, one of the sources of innovation in this industry - big corps, startups, or academic/open source, would have filled it. Even if it required extending HTTP/HTML somehow - these extensions happen quickly when really needed.