I've been following AIR since its early days, and have also been waiting for Adobe to step to the plate and offer a tool to support exactly the type of development you talk about above, but apart from the (now apparently defunct, due to Aptana being bought out by Appcellerator) AIR plugin for Aptana, the only viable option that I can see it to do exactly what you outline -- namely build your js app normally for the browser (all the logic and UI) and then use AIR's bridge to offer your app access to the specific AIR platform functionality that you require.
...I'd personally love to see Adobe offer some sort of slick dev environment á la Flash Builder (solid debugging, build process, work-flow...), but targeted to building AIR/js apps. Our little dev company actually bought Flash Builder a while back, but we don't have the time/resources to move our focus to it (or the desire).
PS. Have also been following Titanium, but although it sounds great initially, it seems to have some serious flaws/handicaps vs AIR.
Titanium has some issues, but it does not block these operations, and has some convenient package and statistic features that look interesting. I've decided to build the app on the browser and then plug in the native menus and i/o stuff before deploying to desktop using Titanium.