Thanks so much for the write-up, Jeff. You're absolutely right, pretty much all of the issues you've mentioned are being actively worked on. The good news is, some of the work I'm doing will be able to go upstream to the javascript library itself.

We have a cool internal project at UBC for which we're developing WP-Side-Comments which means it's going to be actively developed. Whilst I take many of your points re: options/settings, I'm going to try and stick to the mantra of "decisions, not options" as much as possible. Especially early on in development.

The issue of theme compatibility is...tricky. I have a couple of thoughts about how best to approach this at the moment. Standard Theme Hooks is the nirvana, but for the time being, I think there's something that we - as plugin developers - can do to make it as seamless as possible for the end user.

Again, thanks so much.