I would choose YUI over both of those options, given the choice.
I second that... I would even take Spry as a second choice over those others to be honest and it is in pre-release still, but Spry is way nicer looking out of the box and they you can get support questions answered by the developers on their forum because of the fact it is in pre-release and they are trying to get people to use it so they get free testing... I have been impressed.
Scally.... yes, YUI is more robust as it stands now for sure.
Too be honest I have been mixing and matching. I have sites that run both. For example a photo gallery looks way nicer with Spry default then YUI so I went with that for Ajax galleries and form validation is nice looking too, but for other stuff I use YUI.
Like you said, you are thinking long term so no reason not to dabble with both.
As for documentation, the YUI documentation is the best out there. I find the jQuery and Mootols documentation to be difficult to navigate, and more difficult to understand. So in my opinion, YUI wins there hands down as well.
YUI sounds about the best then - i think documentation of things is so important, also the way it looks (the animation side etc). What i may do is try a little on each after working with YUI for a while. I must admit when i saw the moo tools demos it looked pretty slick - that must be what got me on it, i love nice animations in JS.