Right now it appears to be an either/or relationship.
You can't have user talk pages without disabling message walls (which hides them)
You can't have message walls without disabling user talk pages (which hides them)
You can't have article comments without disabling article talk pages (which hides them)
You can't have article talk pages without disabling article comments (it hides them)
These don't really cause problems if a wiki is run consistently one way from the outset, but it can if you switch because then you lose the ability to view these old conversations easily.
Would it be possible as a new feature to simply have 4 boxes to check and to have the option of them simultaneously existing? Like in the drop down why not have both "My Talk" AND have "Message Wall"? That way, some communities could give people both options, to use that which they prefer.
As for comments, I like the appearance just not the bottom-of-page embed, so in addition to the standard "comments forever at bottom", having a comment section appear on a different sub-page (like how article talk pages do) would be a great option too, and could coexist with a talk page.
You are certainly not the first person to think this. In fact, a while ago, I even started trying to work on a way to display article comments and message walls while the features are disabled (see here). However, I was nowhere near as JS savvy as I am now (though I still am not that savvy) so the solution is rather awkward and not even quite done yet.
Because of the way the thread posts are stored, this mutual exclusivity may be necessary; or at least it is precautionary. The issue is that the thread posts are stores as subpages of the respective talk namespaces. What Wikia might be trying to avoid is a scenario in which the ability to edit in the talk namespaces leads to mis-editing/vandalism of the thread posts. But that is just speculation on my part.
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