The templates you refer to are not intended to resolve this issue. Each of these templates is designed to provide basic functionality and demonstrate some of the key features needed in a W3C widget. See See http://markmail.org/thread/275767sda32prucn for the original proposal. So:
basic - a very basic widget demonstrating the recommended structure (which is as defined in this issue)
jquery-mobile - a suggestion on a standard approach for jQueryMobile widgets (they provide the skin/theme)
setting - demonstrates the reading and setting of properties in a very flexible way (i.e. no need to write loads of code)
wave - Demonstration of how to use wave features
s5 - demonstration of how to present slides in a widget
With respect to this issue I recently proposed a solution that provides a templating system to replace the existing one. This new system will address both the functionality templates we already have and the skinning that this issue addresses. See http://markmail.org/thread/scgeyrobljqk7zhz
The code for this new system will be brought into the Wookie scratchpad very soon. It is pre-alpha functional right now and under rapid development. If you want to look at it before I get the time to drop it here you can fnid it in apache-extras at http://code.google.com/a/apache-extras.org/p/rave-in-context/source/browse/ (it's already Apache licensed and I am committed to bringing it here, so you are safe to experiment).
With respect to your specific question "is JQueryMobile the default template" I would say no. JQueryMobile is great, however it is only really appropriate for mobile devices. It works on desktop browsers (for the most part), but some of the interaction mechanisms (like swipe) are alien to desktop. That being said it is possible to build widgets using only the features of JQueryMobile that make sense on the desktop as well as the browser.
The new templating system will (theoretically) be able to replace the UI framework with one more appropriate for your target devices. That is, you would have two sets of templates one for desktop and one for mobile. When you run the "ant generate-templates" command it would build two separate widgets for you.
NOTE: I say "theoretically" because I have no plans to actually implement that at this point. However, it is a direction I expect to go in the future and would welcome input in that direction.