This partly explains the lack of updates to PrototypeJS (last version shipped over a year ago). My hunch is that if they are building something from scratch, they have abandoned Prototype entirely in favor of jQuery.
Basecamp isn't what explains the lack of updates to PrototypeJS. jQuery itself is, however.
It is (MUCH) faster, got traction quicker, has a larger community and is definitely more flexible. Rails moved from Prototype for good with version 3, which was released a little over a year ago - it would make no sense for Basecamp to stick with prototype.
