Side thought:

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?