> introduces no new holes - everything I ask for is already possible when running a native application.
A native application involves downloading a binary and installing it on your machine. Those involve a higher degree of trust than, say, clicking on a random URL. "I will read this person's blog" vs "I will download a binary to read this preson's blog" are acts with different trust requirements. At least for most people.
I suppose in a somewhat ironic way the iOS sandbox makes me feel more comfortable downloading random native apps but it probably really shouldn't! The OS is good about isolating cookie access for exactly the sort of things you're talking about (the prompt is like "this app wants to access your data for website.com)), but I should definitely be careful