Like the responsive design paradigm in HTML5, content authors needs to build content that considers various form factors when targeting the modern web. We explored numerous workarounds for legacy content when building Flash Player for mobile devices, but scaling down content intended for a large-screen desktop device simply isn't enough. We can do some intelligent things with "touch point fudging" to make buttons that are too small work at the smaller scales and stuff, but really, you have to author with smaller form factors in mind if you want a good experience. Like you've seen with responsive design, layout, positioning and styling can be significantly different for various form factors, and that behavior needs to be defined by the developer. We can't simply apply a generic set of rules to the diverse body of Flash content on the web.
The runtime itself actually worked really well on mobile at the end, but it was heavily criticized for not playing content designed in the 90's for desktop platforms in a perfect and seamless way on a form-factor that didn't exist at the time. Having spent a couple years of my life on those efforts, i'm pretty biased, but Flash on Android (and WebOS, and Blackberry) were all pretty great given the state of the available operating systems and hardware at the time.
The main justification for dropping Flash Player on Android was that if you have to re-write your content for mobile to get a good experience anyway, you can author and target content to mobile devices using Adobe AIR, and you'll end up with a native app instead of the device's browser. All of the market research at the time indicated that nobody used the browser on mobile anyway (greatly preferring individual apps), it didn't seem worth it to continue to invest in targeting those platforms with the browser plug-in.
The convergence of the desktop and tablet form factors is basically a replay of what we were going through with Android back in 2010. If content isn't authored to be aware of the form factor on which it's displayed, it's not going to be a good experience on all devices. Flash Player actually returns all of the events and information required to make compelling, responsive content today. We support multi-touch, screen rotation, high-DPI displays, and content can listen and respond to events when the display orientations and sizes change; however, it's up to the content developer to author content that meets the needs of today's increasingly fragmented world of devices, operating systems and form-factors.