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#1 ------:
I think we can tackle this defining a "lazyload" feature per YUI instance. So at the moment you create a new instance, defining new modules and using "use" to load the requirements, the system should wait a little bit before actually inserting the script tag in the page, just to make sure that the next block is not another instantiation process. If it's in fact another instance, we can merge the requirements, inserting a single script tag, instead of 2, and so on. I guess the first step should be delaying the loading process until the "domready" or "load". Merging all the initial instances thru a single script tag instead of 19 scripts tags. Here is an example:

YUI({modules: {a:{fullpath:'a.js'}}}).use ('a', 'node', 'io', function(Y) {});

...HTML CODE IN THE MIDDLE...

YUI({modules: {b:{fullpath:'b.js'}}}).use ('b', 'dd', 'event', function(Y) {});

The optimized result should be:
1. yui.js
2. combo?node+event+io+dd+other
3. a.js
4. b.js

instead of:
1. yui.js
2. combo?node-io-other
3. a.js
4. combo?event-dd-other
5. b.js

One of my side projects (bootstrap: http://github.com/caridy/bootstrap/tree/master) will address some of this issues, wrapping he loader functionality, and providing a similar API for yui 2.x as well. Feel free to dig in.