I'd say either of them would be fine, but there does seem to be more momentum behind jQuery as of late.

Prototype does a lot in that extra 24 KB, is faster on some benchmarks, and I just like the way the code looks. If you just minify and gzip Prototype, you're looking at a much lighter footprint.

In the end, none of the frameworks are very lean: though Mootools and YUI are at least modular.

I know that prototype and scriptaculous provide more functionality, but my point is that jQuery is providing enough of what I need from both libraries while still being smaller.

Seriously though - I've written both and I'd find it hard to go wrong with either. jQuery is more the way I've been leaning of late, but were it to suddenly disappear off the face of the earth tomorrow I'd be fine with Prototype/Scriptaculous. To each, his own. :-)

I actually find both to be a bit heavy. I don't necessarily want animations out of the box, so that makes jQuery a bit more bloated to me.

I also don't necessarily want all that Prototype offers for all of my projects.