On the contrary, it appears further discussion might be helpful because there still does not appear to be an understanding of the complexity of this matter. The suggestion to "add a UI button to turn Mootools off." would be irresponsible. It would cause problems for users. I really want you to understand this - because I am confident when you do, it will make sense to you why we are here, and how this is resolving in the industry, and that you do have options (whether you use Joomla!, or WP, or Drupal, etc.) to offer a thin client approach.
Patience with my explanation, please.
Mootools comes with Joomla!. It is not developed as an option, it is crafted as a core feature *expected* to be on. The core code base relies on Mootools. Turning it off will cause problems. It would be analogous to adding a feature that allows you to turn off the router. While it is indeed possible to disable the router functions from running, the Web site would no longer work. Think in those terms since that is the reality of the matter.
Why do I say that? Well, at this time, and especially when the decision was made to include Mootools, JS Frameworks are (were) notorious for not working well together. It's not easy for those less technical to resolve issues of framework conflicts. For that reason, the developers decided to protect end users and reviewed and selected a framework, integrating it with Joomla!.
Bear in mind an important second factor. The core developers would also like to offer JS enabled functions in the CMS. Thus far, core functions are largely restricted to the Administrator (tabs and sliders are examples of this capability. There is also a small amount of Mootools-enabled Ajax in the Installation process when the "Install Sample Data" option is selected.) There is, at this time, only one JS feature in the Frontend, and that is the "captions" option. So, in order to include JS functions in core, the core must have a JS framework.
I don't think *any* widely used CMS comes without some core JS framework. WordPress and Drupal come with jQuery. Drupal 7 will have jQuery UI, too. It appears WordPress is also heading in that direction. So, this is not unusual for a CMS to have a JS framework hardwired in it's core. JS functionality is expected today. In order to provide that capability, you must have JS available. No way around it.
In 1.6, we will enjoy a new Comments Extension which is currently a commercial product offered by JXtended that they are donating to the community. Those most knowledgeable about technology features will agree that Ajax is an important part of new technology. The Comments Extension will sport Ajax-enabled response and rating elements.
However, do not fear. If you do not wish to use the JS elements, you will not be required. Simply use the three lines of code I shared in your Template - or install an extension that turns the JS off - or - obtain a Template that does this for you. The comments feature will continue to work without the advanced (and cool) capabilities.
Also, be encouraged to know that frameworks such as jQuery and now, in the latest release of Mootools that is already in the 1.6 base, ability to prevent framework conflicts is part of the JS framework. So, we should see flexibility in the coming years when dealing with this problem. Also, it is getting to be a commonly accepted development practice to build JS and Ajax functionality as an "add on" to the code base. That means well developed code will continue to function even when the client's JS option has been deactivated. So, again, this problem is sorting in the industry and will likely be a non-issue when we get to 1.7, or 1.8, at the latest.
In sum, Mootools is part of Joomla!. It is intended to be hardwired into the code base. This decision is based on two important factors: setting precedence for third party developers to use the same framework in order to eliminate conflicts in frameworks for end users and 2) to provide JS capabilities for the core developers to use within the core Joomla! source. Until there are other ways to accomplish those two goals, Mootools will be part of the core.
Having said that, we can enjoy the full benefits the GPL offers and turn it off if we choose. The methods for doing so include adding those three lines of code to our templates or installing an extension for that purpose. Once we do so, we must also be able to manage dealing with functions that no longer work due to the fact we disabled Mootools.
Further, the future looks bright as the industry as a whole is grappling with these problems and the JS Framework folks and developers are all working hard to ensure frameworks can peacefully co-exist - and applications continue to function - when the JS is turned off.
Heading there. Just not there yet. But, we will get there, that's a guarantee.
Hope that clarifies the situation further.