My fear is, and I believe it is a lot of other peoples fear, that one day LQT will be incompatible with some future version of MW. This would be an end of story for the wikis utilizing LQT.
However, my impression is that there are quite a lot them around and still counting. This is due to the fact that even the current life supported version of LQT is far better for talk pages than any other solution around (including plain talk pages with no thrills). Besides, LQT was and still is one of the coolest things that came out of development during the past five years.
Basically the problem is, and this is the major cause of emotions here, that all these wikis do not know what to expect with regard to LQT and are being left alone for quite some time now. They are stuck in the darkest uncertainty regarding their wikis.
LQT is beyond the point of no return. We know it, WMF knows it and this is the very big dilemma.
I won't go so far as to say that it is "beyond the point of no return," but I understand your fears and it's reasonable to have them.
I don't think the goals of messaging can replace LQT. In determining editor engagement and features goals, it was clearly obvious that user-user messaging is broken so a project was put in 2012-13 goals to address that. This has been named "Flow" and according to planning will not be worked on directly until early 2013 (all work beforehand is infrastructural, and UI/UX resources are prioritized around notifications).
I want to emphasize that improving User Talk (user:user messaging and discussion) is a fundamentally simpler structure of interaction and requirements than Page Talk or LQT which is many things to many wikis (from a Talk replacement to a full blown forum and discussion system). At some point, things move beyond user-user to discussions, and I (personally) think that LQT rework to incorporate the core architectural and feature changes (Echo/Flow/Global Profile) is closer to a solution here than upgrading/changing a user-user messaging system like Flow.
There are no formal resources for LQT development in this year's planning (there are no formal resources on Flow for half the fiscal year). However, the same people involved with Flow are the ones who have worked on LQT which means that there might be some design guidance and bug prioritization for what needs to be done here and it can be kept up-to-date. (I've tried to give the developer the freedom to update LQT code under the auspices of working on Echo and Flow.)
Be aware mediawiki.org currently uses LQT without any plans on that changing. So while it doesn't mean you'll see LQT on English Wikipedia any time soon, this should keep LQT tracking some of the new features being developed (notifications, at least). Finally, probably the best bang for the buck on LQT improvements would be after the new Visual Editor is integrated in MediaWiki. That won't happen until sometime in 2013 anyway.
As for the WMF resources and the mediawiki community at large. This is part of a large discussion on what is and isn't working with respect to integrating changes coming from the developer community, which is broken far worse with more extensions than LQT. I'll follow whatever comes up from that.