The advantages you mention are now mostly possible already using an AMD loader, at least with requirejs. It allows you to load multiple jQuerys and get a handle on them with the multiversion support:
http://requirejs.org/docs/api.html#multiversionso for your code, you do not need to call noConflict, you get a reference to the one you want.
jQuery still needs to export a global because not all jQuery plugins call define() to get a handle on jQuery. While I would prefer that, it is not realistic to expect at this point, so for those cases where an AMD loader loads a jQuery plugin that does not call define(), jQuery still needs to be available globally.
There are two kinds of jQuery plugins:
1) Attach to $ because they did not want to create a global, but just indicate it is jQuery-related functionality. They do not do anything with node lists though.
2) Attach to $.fn because they want to participate in the chained API style when operating with a node list.
Ideally, the #1 cases could detect for AMD, and would call define(['jquery'], function ($) {}) and then just return their functionality from that factory function instead of attaching to jQuery, because the module system gives them a way to export their functionality without needing to pollute another object.
For case #2 though, I still think it is appropriate for the plugin itself to attach to $.fn since it will participate in the chained API calls, and the developer should not have to also then depend on another module that wires the plugins to $.fn.
With the requirejs 2.0 map config:
http://requirejs.org/docs/api.html#config-mapit should be possible for a developer to set up a map of modules, so that for one set, it could create a jquery-adapter module that calls jQuery.sub() to create a contained jQuery for use with some plugins and a different adapter that has a different jQuery.sub() for another set.
In summary, I think the AMD loaders are responsible for handling some of this functionality, and then the other part is educating jQuery plugin authors on the options they have when AMD is available, particularly for the plugins in set #1.