After upgrading from 5.3 to 5.4, and playing some more with jQuery inclusion/placement/etc. I came to realize (probably as others might have, already) that one nice solution (for at least a part of this issue) might be the following:
In the existing widget Java Script Embed Control (found in page edit mode under widget toolbox as Scripts and Styles as Java Script widget), there could be an option to include jQuery, jQuery UI, etc. These could be list of checkboxes underneath the radio buttons for "Where to include in HTML" (head/wherDropped/beforeBodyEnd) section. The new section could be called "Libraries to include" with a list of checkboxes for JQuery, JQueryUI, etc.
The assumption being that, if you're linking to an external js file or embedding some js text right there in the widget, either of which rely on jQuery, for example, you'd have an option RIGHT THERE to tell the widget to also pull in the needed libraries.
Similarly, when using the widget in your own user controls, you could do something like this:
IncludeJQuery and IncludeJQueryUI would be optional (they would default to false, unless specified otherwise).
This way, you wouldn't have to include JQuery in master pages, and you'd have a way to ensure that it's pulled in alongside your jquery scripts ONLY where they are being needed.
Anyways.. perhaps this has been discussed already... But it was a bit of an epiphany for me. Unless I'm missing something... :-)