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.
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.