If you're running Flash content on a page, Flash is going to be running an event loop at the SWFs frame rate, even if it's not actually doing anything. JS, on the other hand, can be totally idle when it's not running any code.
Most JS use is sparing and lightweight and more about interaction than action/animation. Most Flash use is heavy-handed, ham-fisted, and overbearing, done more for cosmetic effect than additional function. Is this a part of the technology? No, but it certainly is nurtured by the differences between the development environments — Flash is still sold as an animation studio! What's more, JS gets to manipulate the DOM directly, giving it a much nicer relationship with the typical web experience than Flash, which is effectively a replacement for the DOM.
Have you used Twitter or Facebook on resource constrained machines? Even on latest nightly builds of Chromium it's painful on my Dell Mini netbook.
The point is that you can use Javascript do just about everything you can do in Flash. And Adobe CS6 will almost certainly contain some tools to help you use your existing Flash assets in a pure JS+HTML+CSS environment. So the animation studio for Javascript doesn't exist yet, but we're talking about the near future where it will and it will be just as obnoxious as Flash (but much harder to block from consuming CPU.)
The new Twitter really is the worst, and it's not just the Javascript. They've got that hovering topbar with an RGBA shadow and gradient background, which I've personally verified as being a source of much of the slowness on browsers that support these things. You can test it for yourself in any Webkit browser or FireBug — just disable those two CSS properties, and new Twitter feels immediately snappier.
Imagine what Gmail would be like if they went overboard with CSS.
Most JS use is sparing and lightweight and more about interaction than action/animation. Most Flash use is heavy-handed, ham-fisted, and overbearing, done more for cosmetic effect than additional function. Is this a part of the technology? No, but it certainly is nurtured by the differences between the development environments — Flash is still sold as an animation studio! What's more, JS gets to manipulate the DOM directly, giving it a much nicer relationship with the typical web experience than Flash, which is effectively a replacement for the DOM.