I think the main problem is not the application software (aside from iTunes and Apple Maps) - the main problem is the OS level software.
During the "golden age" of apple, apps would just work. Didn't matter if it you were using Apple-provided software or "better" 3rd party stuff - crashing, lagging, stuttering was minimal.
Now, many users are seeing much more lag, beach balling, and kernel panicking than before, across all of their applications. [1] Combine this with some poor decision making in the UX/UI department of certain Apple apps and you get a lot of people who are unhappy with their entire software stack.
But the app is the closest piece of software to them, so instinctively it makes more sense to blame declining app quality, when it's actually more a function of OS stability.