VS2012 took out installer projects (instead telling you to just use InstallShield), SQLCLR projects, was incompatible with Oleg Sych's T4 Toolbox plug-in, and had a colour-scheme in the TFS source browser that made my eyes want to bleed. Every other VS upgrade has been comparatively painless. I can't say I'm excited to try VS2013.
For installers, use http://wixtoolset.org/ .
Considering how thoroughly MS screwed the pooch on ClickOnce, I was genuinely surprised when they completely abandoned their working installer system.