They're handled differently in at least 2 ways:
Monkey Ball is 3D, using OpenGL and leveraging the 3D capabilities of the GPU hardware, while Flash is its own 2D vector engine.
Monkey Ball and OpenGL are not made be Adobe. Flash is

And Adobe has long allowed Flash to be less efficient on non-Windows platforms. That needs to change.
Yep--a necessity. Both for sites with annoying ads, and for battery savings, and potentially for security if some bug should be discovered in Flash again. I expect Apple would indeed allow plugins to be disabled, just like with desktop Safari.
By the way, if anyone thinks the "death of Flash" (not happening anyway) would be an end to obnoxious banner ads, they are crazy.
The problem is not Flash, the problem is advertisers... and they are the problem that pays for your Web, so they're not going away.
If Flash were gone, advertisers would STILL need to get your attention, and they would do so by other technologies. With the same obnoxious results.
Saying Flash is a "problem" and the absence of Flash is a "feature," just because of ads, makes no sense. Take away Flash and the same ads would be back overnight.
In fact, if the iPhone keeps taking off and Flash does NOT arrive, then sites will start to target iPhones with non-Flash ads. (Sproutcore? Animated GIF? .H264? Whatever.) Using the absence of Flash as an ad-blocker cannot last forever.
In which case, give me my Flash games and my Flash menus and my Flash video!

They don't even have to load slowly--that expectation comes from a few bad apples. (The problem there is BADLY done Flash. And any other technology can be implemented wastefully too.)