Flash didn’t allow arbitrary code to run. It had a very limited scripting language (which design-wise is superior to JavaScript, by the way) to control canvas elements and playing sound. You couldn’t execute programs on your computer.
If by late you mean right before action script 2. I was making flash games back then and I remember it being unable to access virtually anything without first triggering a prompt, which you could disable by right clicking, and going into properties.
Your legitimate concerns about JavaScript are blockable by the browser.
Yes, through NoScript. And it should be blocked, not blockable.
It is funny you mention evercookie because that was a JavaScript library, and affected all cookies, not just flash cookies.
Flash cookies being sharable between browsers was bad, but you could still easily clear those cookies, that is until a certain JavaScript library started restoring them automatically.