@CarlHead: You can't really have Windows Store apps* on the Taskbar, because the entire point behind them is that they are conceptually always running, even when they aren't actually running. To represent that on the Taskbar, you'd need to have them all visible, all the time. That would make the taskbar unusable. It would also be completely counter-intuitive, you couldn't "unpin" them (because they're "running") or use the Taskbar to meaningfully keep track of what you're doing (as some people suggest it should).
The only place I find it annoying at the moment is moving between IE one the desktop and IE Windows Store app* and I only ever have to do that because of the weird and arbitrary decision over Flash. I'd love to believe Flash would disappear overnight and then it would be a non-issue, but I don't see it happening and really think Microsoft need to reconsider that, perhaps moving to a blacklist rather than a whitelist for Flash in IE.
*Yeah, that name really works, doesn't it?