I recently started doing a lot of JS and found prototype to be a lot more useful. I've used jQuery only a little bit, but Prototype v1.6 seems to be able to do everything jQuery is good at (DOM traversing and manipulation) and has other useful things like a extended arrays, hash maps, ranges, classes/inheritance etc.
The web framework that I use (Weblocks) is built on prototype, but it only uses a small subset of the code with no reason to send 120K (uncompressed/unminified) over the wire. I think the next step is to use a code coverage tool to strip out all the unused code, which is a project I'm hoping to get a little time on soon. This should (back envelope calculation) reduce it to less than 25K.
jQuery also plays well with Prototype, so, with stripping, I'm hoping to try using both. Best of both worlds?
Mootools lets you do it; you can even choose the type of compression you want (although I prefer to minify things myself): http://www.mootools.net/download
but to add some value to the discussion with my post, i'd like to show you some metrics. usage numbers have them essentially tied, when last year prototype was far in the lead. http://ajaxian.com/archives/nitobi-survey-results-on-ajax-de...