Then, there is the issue of hardware. The 3DS is not exactly cutting edge performance wise, and even on a much more powerful device like the iPhone 4 (which supports HTML5 well) the performance is still what I would consider unplayable for any game that has a lot of motion and moving objects.
It's just unrealistic to expect that the 3DS would somehow perform better than iPhone/iPod with significantly slower hardware.
On my work PC with integrated graphics, i get 60fps on a demo. that same demo on my iphone 3GS gets about 15 frames.
iPhone has an artificial speed limitation for HTML 5 apps in the browser, so that HTML5 applications bought from the App store perform better and Apple can control what users run on their iPhone.
BigBrother strikes again.