Here are my thoughts on JQuery vs. Prototype - I do not think either is better. It's just a tradeoff based on your needs and team.
More Active Community
More Active/Verbal Maintainer
More concise code
Cross-browser support is not so great
Dom centric programming (not so easy for Java folks to wrap their heads around this)
No class support or inheritance (again, odd for Java folks to wrap their head around this)
Amazing cross browser support
Low memory footprint (compared to other frameworks)
Great Object Orientation/Functional based programming (easy for Java/back end developers to jump in the game)
More readable code
Better security awareness/responsiveness for Ajax functionality
sizable download file
not as concise as JQuery
community not as active (at times)
Summary: Most designers prefer JSQuery. Most Java Programmers prefer Prototype. But if you would like to have your cake and eat it to, then use both, together.