According to Aaron Newton of Clientcide, this is not the question to be asking.
And I happen to agree with him.
These two frameworks just aren’t trying to do the same things. They overlap in the functionality they provide, but they are not trying to do the same things
Opposite Directions
MooTools is aimed more at JavaScript developers, while [...]

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Before you fans of JavaScript libraries (e.g. jQuery, MooTools, Prototype/scriptaculous, etc.) form a mob and beat me to death with your coffee mugs, let me quickly state that I am a BIG fan of JS libraries. They make life much easier in most programming scenarios, BUT…
Sometimes using them for smaller JavaScript tasks and effects [...]

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