The defacto-standard already seems to be happening with Twitter Bootstrap. Give it another few years and I expect this will spread into more well-known apps (or the current startups using it will become more prominent).
And I do think people are addressing the other issues. Chrome's Web-App API can open pages in new windows without the browser UI, and Firefox is due to have their similar API available soon.
Things like keyboard shortcuts will likely sort themselves out eventually: for example, Github's issue tracking tries to mirror the keyboard shortcuts of gmail wherever the actions are similar.
And I do think people are addressing the other issues. Chrome's Web-App API can open pages in new windows without the browser UI, and Firefox is due to have their similar API available soon.
Things like keyboard shortcuts will likely sort themselves out eventually: for example, Github's issue tracking tries to mirror the keyboard shortcuts of gmail wherever the actions are similar.