I've recently switched to jQuery from prototype. I just got fed up with prototype + scriptaculous' ever increasing file size - up to 300Kb for the whole thing, which is ludicrous for what I'm using it for - I probably don't even use 1/10th of the functionality but my attempts to slim it down to just what I need failed since every bit is dependent on another bit.
jQuery on its own is about 30% smaller than prototype and they provide minified and packed versions for you. (plus prototype can go a bit funky when you try to minify it)
I also find the the jQuery documentation is much better. I've never really used the prototype docs site because its basically unusable, I've never found anything helpful there