Since JQuery is such a small addition to your assembly wouldn't it be nice if a developer could select what version to use. So as a property I'd like useEmbeddedJqueryVersion with enums of 1,2,3 or none. This should also give you feedback on what controls need updating.
The script tags should contain "defer" attribute. Resolution: You can set the LoadScriptsBeforeUI property of the script manager to false so that the scripts will render as late in the page as possible (just above the inline <script> that MS AJAX generates for the $create() statements). This will provide benefit nearly identical to the defer feature, but it does not risk breaking existing functionality. More information on the property: https://msdn.microsoft.com/en-us/library/system.web.ui.scriptmanager.loadscriptsbeforeui(v=vs.110).aspx
I hate the stupid asp script managers...they're so ghetto with the .axd files always hosing our yslow\pagespeed scores, etc. Since your focus is no on css3\html5\lightweight rendering can you guys not come up a better way to bundle your scripts such that they render properly cached to the footer...maybe take a dependancy for that on system.web.optimization or something? ...maybe some sort of requireJS integration or...? Please feel free to think out of the box instead of being stuck into the asp.net crapballs bloat framework.