We had been using the theme builder plugin in Confluence 3.0.1 for some customized spaces and we are upgrading to Confluence 3.5.17. We have decided to stop using the plug-in. The main two reasons behind our choice are css needing a large amount of patching (having to set a property for almost every element) and the plugin breaks IE9 support badly in the spaces that the plugin was used. We switched to editing the velocity file and css in the layout section of the space admin now to customize the layouts.
At a quick glance, we did look at the themebuilder plugin in Confluence 4.0 and it seemed to work much better than our current expirence with 3.5.17. My recomendation is to not customize a space unless you have to as (with or with-out the plugin) it complicates upgrades.
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