I'd like to shine some light on the background of the ins and outs, clear up some confusion, and maybe provide some insight into why we believe this is one of the better decisions we have made since the start of Kunena.
So we wrote code with that between components like JomSocial and Kunena would result in the load of only a single copy of the libraries.
After dealing with these issues for many months and countless forum threads that last to this very day and after talking to various Joomla core developers and architects we came to the conclusion that we have been at this totally wrong for the longest time.
Now, we cannot fix all the other software out there and it is certainly clear that there is a lot of low quality modules and plug-ins around. That is not to say people don't mean well, but some pieces are just hacks from lesser experienced developers, or not enough thought has been given to the overall architecture. And by God, we do realize that we inherited a lot of junk ourselves.
With the evolution of Kunena 1.6, it was another goal to write it so it will run on both Joomla 1.5 as well as Joomla 1.6—once it is out there in a stable form. That plus the fact that the original Joomla 1.5 came with the now-outdated 1.1 version of it, made us think through how to go about this. Luckily MooTools & Joomla came forward with a legacy module that allows older applications to run on the newer 1.2.x version now shipped with Joomla. Its just like the legacy module for Joomla 1.0 code to run in Joomla 1.5. Even with that legacy module, not all Joomla 1.0 applications would run under Joomla 1.5—as we learned ourselves in the early days of Kunena.
We also watched very closely what other developers were doing and how their products progress. Some of the most prominent names in joomla software and templates have already migrated their code to be native to the new MooTools 1.2.x framework and if you run their software and templates together with Kunena 1.6 you will end up with an awesome out-of-the-box experience. Some other templates (in most cases, outdated menu code) and modules will cling to the older libraries because they believe they can get away with it. Ultimately, those that only work in legacy mode will have the same reputation as components that only ran in 1.0 legacy mode.
We were late getting to Joomla 1.5-native and we have learned our lesson. MooTools 1.2.4 is the future of Joomla 1.5 and 1.6. Kunena is about the future of forums in Joomla and their latest releases. As such we made the decision to invest into the right future for Kunena 1.6.
If, in your case, you are not ready to upgrade your site to the new standards, we will continue to support Kunena 1.5 until a later date when the vast majority of users have upgraded and migrated. Kunena 1.6 is about new features like, for example, a completely rewritten bbcode editor—one we wrote from scratch based on a MooTools editor library and that is one of the most advanced non-WYSIWYG bbcode editor out there. We also invested into multi-file uploads that are super easy to use and feel natural, yet don't require flash and other plugins to work.
Hope this explains why we are where we are in regards to MooTools.
Here is some more information about Mootools: Javavascript and Kunena