[eluser]HdotNET[/eluser]
The main thing for me is always filesize, and mootools wins on that front in its modular approach to the way you can build the library.
Jquery / Prototype both weigh in at around 20kb but can do more out of the box.
I can't answer as to how well any would fit into CI, but I'd imagine that depends on your application more than anything.