Flash was always very buggy. Perhaps you didn't see them if you kept to a strict web developer subset of Flash. But the problem was that it had a different set of bugs on every platform. I guess that codebase was very old and could have been shared better between platforms. So at least for for non-Windows users that meant the plugin crashed daily on whatever input you happened upon on the web.

It also had (and still has) an enormous set of language features, a billion codecs, a handful of protocols and several different scripting languages, a vanishingly small subset of which was still maintained. The result was probably the most insecure software ever to grace the face of the Earth. Running by default. Taking input on every web page you ever visited.

So it was never just a "marketing controversy". Sure, Apple and Adobe could never agree on the terms for flash on non-Mac devices. But that alone would never have been enough for the demise of Flash. Google, and to a lesser extent Microsoft, did large parts of the work. They were rightfully concerned not just with Flash as a vector for malware, but also the power it brought to Adobe who could single handedly decide what Flash would run and on which platforms.