Redesigning the site is always planned and often gets worked on already (and quite a few changes are already in production). But, no, this change really has nothing to do with that.
I was thinking of creating a Quest for HTML design for the site, concentrating on how a thread with nested replies should be displayed. I mostly find PerlMonks' display of such to be easier to understand than most other forums I've looked at, but there are several specific places I think could be improved (space wasted by "[reply]" links, move votes to the bottom of nodes, more support for customizing via CSS, vertical lines to make nesting easier to trace, ...).
ar0n started a redesign, but it was more toward just CSS issues and, as I recall, wouldn't support non-CSS browsers as well as our current layout (and the more I learn about CSS, the more I think we shouldn't degrade the presentation for non-CSS browsers just because we are making customization via CSS easier).