With bundles I don't know if the software has been tested on my architecture, if it's stable, if I'm downloading a botnet, if it comes with bundled libraries or if it works properly with -fpie and --as-needed.

Then you have software that doesn't have official releases (like half the stuff on github)

I'll stop using a package manager the day that all ruby gems work with MRI 1.8, 1.9, JRuby and REE. Basically, never.