Why I prefer JQuery to prototype/script.aculo.us?

Because it's more pipe friendly, more powerful to traverse the DOM tree and last but not least more maintainable.

1. pipe friendly: Like unix pipe, you could select amazing complicated elements using chains of filters like this: $("a").addClass("test").show().html("foo");
   
2. powerful DOM traversal: Still use for(var i=0;i to loop through your list and do something to the parent elements? That's so quaint compared to this $("div#nav span").parents("p").attrs({'font-weight':'bold'}). Image what could be done by combining this with "chinas of filters"!!
   
3. maintainable:I was totally blowed away when I first saw jquery's selector syntax. Simple it is, but it allows we use the same CSS/XPath selector syntax in javascript. Combine this with "DOM traversing" parents, prev, sibling and "Filters" like lt(5), eq(0), gt(4), contains and you could do magic with only one line of code. Yet more readable. CodeEye also mentions a couple of very nicely constructed, highly readable selector here and a very nice, neat FAQ page built using jquery at here.
   

Yes, do everything with one line of code and make the code more readable. This is the magic of jquery.