Considering how thoroughly MS screwed the pooch on ClickOnce, I was genuinely surprised when they completely abandoned their working installer system.
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...
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.