I tried to use few plugins to enable/disable the UNBELIEVEABLE heavy mootools, but everytime it's a pain in the..... because joomla core functionalities sometimes don't work and other extensions using mootools don't work correctly, and I'm always wondering why (like you just said) there are so many coders defending so hardly mootools, when jquery is simple, fast and effective but first of all lightweight.
I'm awaiting to see the new joomla release to see if they are really moving in that direction, otherwise I'm seriously thinking to fork joomla on github and remove all the mootools code ( step by step, in my spare time ), I'm a bit tired of it, and maybe integrate the jdom by default
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I was also wondering why JDOM is not on github, I think it would have a bit of help from other coders.