Considering how thoroughly MS screwed the pooch on ClickOnce, I was genuinely surprised when they completely abandoned their working installer system.
Problems:
* Can't choose installation path * No offline installation * Hard (impossible?) to use with a CDN.
Here's an example of how to turn a directory of precompiled binaries into a click once package using powershell:
https://gist.github.com/jonnii/2628150
My powershell isn't _great_, so forgive any powershell oddities, but notice how much you have to massage the output of the mage tools to actually get it to do what you want.
There's also no ability to publish the built installer outside of the UI- my build scripts had to build the /app.publish directory and then just copy the whole shebang to a network location for deployment. I'm not as upset about this being a separate step, but if they indeed allow you to configure and deploy the installer from within the UI why not expose an API to do it as well?
Overall I think ClickOnce is fine for internal, self-updating tools. It's worth noting, however, that I was inspired to create my workflow based on looking at what Github was doing with their windows client.
[1]: http://whazzing.com/blog/2013/04/11/automated-clickonce-buil...