Switching themes with customized templates

Most typical Apex applications start with a quick prototype containing most of the required functionality, get required approvals, and continue building it up.
During all of this, the concept of "themes" is mentioned and demonstrated as a reassurance that the "look and feel" of the application can be very easily switched at any point. In other words, let's worry about designing the content and behaviour, the presentation can be easily switched.
All this sounds very good on paper and is do-able as long as one uses the out-of-the-box Apex themes/templates. But, in my experience, any non-trivial application has lots of customized templates. That brings me to my question.
As soon as you start to customize templates, modify them, create new ones, etc, you start to get "committed" to that specific theme. In other words, if I have a theme with 10 customized templates, 5 slightly modified ones, etc, and I switch to another theme from the Apex repository, I get all the out-of-the-box templates for that theme. I have to painstakingly re-do all my customizations for the corresponding templates in the new theme.
And Apex does nothing to help me with this task. There is no "diff" utility between themes, no compares, no merges, nothing. I have to eye-ball the old template, copy the HTML snippets from the Builder into Notepad, pull up my new template and manually copy, paste, modify snippets into the new template. Very error-prone.
How have people handled this sort of thing? Are there any best-practices, any procedures that people follow to make switching between themes painless?
Thanks

Hello,
Second post down.
http://wiki.shellprompt.net/bin/view/Apex/ThemeTips
I build out themes all the time that are about 70/30 standard templates to custom templates and following that procedure makes the switches fairly easy.
Carl

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