Reality check
I think the problem is mostly cosmetic. First I think the "new message" text is to tightly woven with the conception of messages specifically to the user. You don't expect "new messages" to show new messages to other people. The other issue is the numerical count that keeps changing/going up. This makes it hard to ignore, and feel the need to "sort them out." The watch list does not alter the cosmetic look of the site and changes are easily ignored.
These two things combined make it feel far more intrusive than the old system.
I'll agree with that. Again, it comes back to the whole "automatically watch pages I post on", which is very useful with the present system. Watched stuff with new messages is displayed differently on the Watchlist or RC, and you can pick and choose as you like.
But say this gets put in general use as-is. Then you can no longer go "oh, that's Nx's talk page where I put a casual message a few months ago, I can ignore that". It's stuck in with everything else, and you've got to sort through it. Either that, or remove that page and others like it after every random message, which is pretty damn clunky.
One advantage that the current system does have in that sense, it occurs to me, is the edit summary system. A lot of the time it isn't used, but at least it usually shows whether it's a section of the page that I care about or not. So again, maybe there's a conversation on Nx's talk page I wanna know about, but I don't care about the programming-related ones. With RC/Watchlist I know beforehand whether to bother with the conversation. Not so much with LT, since it all gets tossed in one big "new messages" bin.
Now if there was some way to deal with issues like that, it wouldn't be much of a problem. Not sure how it'd be done, though.
Replying to myself here, but I'm looking at that summary at the top of your screen. I wonder if maybe the default for LQT could be changed to a collapsed summary version (at least thread titles) when "New Messages" is hit. That'd make it easier at least to sort what conversations you want to bother with and which you can safely mark as read without further investigation. It'd certainly be an step in the right direction.
You can unwatch my talk page, then watch individual threads so you only get notified of new replies to those threads. In fact this is how lqt is supposed to work, e.g. you start a thread on my talk page asking me something, you want to be notified when I reply to that thread, but you don't care about the rest of the stuff on my page.
One thing that LQT can't do is watch a page, but ignore specific threads. That would be useful on the Saloon bar for example, where you'd want to watch the page in order to get notified of new threads, but be able to ignore threads that don't interest you. I'll try to implement that.
If I may give my personal input, one of the advantages of LQT that I love is that I no longer have to scroll through 6 months of talkpage stuff to get to the newer edits. Instead, it gets bumped right to the top of my talkpage. To me, I prefer this over the old system, because it's akin to prioritization of talkpage edits based on how old they are.
