I\'ll keep this simple.... on my product pages I need to remove the prototype.js file and replace it with the latest version of prototype. So far using local.xml I have successf
Since local.xml is loaded at last by the magento system, so the xml mentioned there are merged at last. That may be the reason that your new prototype is loaded below other scripts.
Alternatively, you can override the Mage_Page_Block_Html_Head::getCssJsHtml() method and play with it.