Prototype to me is a great framework because it is easy to understand the syntax. For me it is terse but not to much. Jquery is a great framework but seems to be very cryptic sometimes. Prototype might be a little more verbose but it pays off in the long run; for understanding the code and managibility in the future.
Let me say from some investigation done on the web that Jquery is more of a took-kit as opposed to a true javascript framework like Mootools. I think Prototype lies between both Jquery and Mootools in that regard.
Prototype does all the dom traversal like Jquery maybe a little more verbosely but it also allows you to do a lot more with the base prototype as opposed to the plugins and extension that Jquery requires.
What do I mean?!
Well when you learn Jquery you aren't really learning Javascipt you learning that toolkit.
If you decide to tackle Mootools which has a bigger learning curve then you are actully learning how to right Javascript within the context of the Mootools library.
An interesting article on Prototype and Jquery merits one developers choice to stick with prototype. blog.thinkrelevance.com/2009/1/12/why-i-still-prefer-prototype-to-jquery