I think that CSS is the biggest failure here. Let's say I have a blog, so for article page markup should be something like this:

    <html><head></head><body>
        <article>lorem ipsum</article>
        <nav></nav>
        <form>search</form>
        <footer></footer>
    </body></html>

That way screen readers, search engines, etc will get the important stuff first and less important stuff afterwards.

But since the common way of presenting blog is more like this:

    <nav></nav>        <form>search</form>
    <article></article>
    <footer></footer>

I either have to do some hacky position:absolute things, crazy floats with negative everything, or just reorder the markup. Crazy and hacky is not fun to maintain, so I have to reorder the markup. That's because CSS is made for changing fonts and colors, and not for layouts.