I don't think there's much memory tradeoff between CGI::Application and separate modules. You should be preloading all of this in startup.pl so it gets shared. Personally, I like to separate functionality into separate modules according to major site functions. For example, I might have a module for updating your user settings, and another one for browsing one of the data types published on the site. I also model the data objects as separate classes, so these modules I'm talking about are really just the "controller" part of a model-view-controller design.
As for XML, I have found uses for it in data exchange but not in page generation. I just can't see the compelling argument for it. TT2 templates are easier to write than XSL. It's trivial to write a template that spits out an XML version of your data for a feed. Validation - well, TT will not compile an invalid template either. I can't see a good reason to use the much slower XML approach, except maybe to plump up your resume.
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