Similar problem with IE for me. I raised a case with gold partner support when IE9 came out as it broke ClickOnce download prompting. Been bouncing back and forth between framework and IE teams ever since.
Result: we now have to ship a .reg file to our clients before we can launch our shit via ClickOnce. That's only 2000 people we now have to hand hold through this.....
Why did they get rid of Installer Projects? We are still on VS2010 and although it isn't a massive issue to use a different installer system, it seems a very odd decision. I mean, you are writing apps for their OS using their tools. Why wouldn't you want to create an installer? Daft!
We know they stink, but it's what a lot of people have spent time working with.
There is no straightforward migration path from vdproj to WiX, either. It's a case of re-writing all of your deployment code (which has already been tested/tweaked/hacked on for years) for no upfront benefit.
WiX is missing all the ease-of-use features it needs to be a non-agonizing process. Deprecating installer packages in favour of WiX would make sense if they provided a migration path and better tooling for WiX.
You get Windows Installer packages, so you can deploy applications via group policies, you get other niceties, like pretending an application is installed until it's actually used (and install then), you get proper transaction support during the installation (something I've seen very many NSIS installers get wrong – maybe that has changed, but not cleaning up after yourself if a step during the installation failed is not how to write an installer).
Result: we now have to ship a .reg file to our clients before we can launch our shit via ClickOnce. That's only 2000 people we now have to hand hold through this.....