Finally I've found some time and implemented a new feature for the FrontCompiler project.
Reconstruction happens pretty quick, almost unnoticeable. And this gives you extra 20-40% of compression over the usual front-compiler compression, which as we all know is already better than the YUI compressor's.
Say the latest Prototype v184.108.40.206 was compressed from 138 kB to 59 kB. MooTools was compressed from 98k to 50k, etc.
You can grab the latest, already compressed files here http://stcamp.net/share/prototype/
Try it, it's just awesome!