I was just about to ask this question, but there seems to be some differences: loading of remote data (I believe in chosen you have to hook yourself the ajax part), the infinite scrolling is also a good idea, and the drag & drop sort was missing.
Chosen doesn't support adding tags dynamically. It also looks like select2's api is more friendly and convenient. I will be converting my chosen dialog to select2 as it looks like an improvement overall.
I chose select2 for homehelpnow.com.au because of paged ajax lookups. Check out the place search box on homehelpnow.com.au. Its AU-based, so might be a bit slower for you US folk.