Update:
As of today, I've pulled rails3 into master, so that's not the main active branch. Also released a new version (2.0.0) to Rubygems.
As for your question; it's hard to say. The jquery branch is pretty stable, except for those few bugfixes you mentioned. The problem with merging it in is that any existing apps (like, say, Curbly.com) will have a pretty rough upgrade path since the jquery branch changes so much of the underlying html. In particular, apps with modifications or overrides to the view templates will have a tricky upgrade in store for them.
I'd love to hear suggestions for how to eases this pain for people. My tendency right now is to just leage jquery-bootstrap where it is (if someone wants to pull in bugfixes from master, that'd be cool), and let people choose it as a starting point for new apps, or upgrade existing apps over time.
Thoughts?
Bruno