The default stylesheet was changed in HTML5 (see http://www.w3.org/Bugs/Public/show_bug.cgi?id=10815) to specify unicode-bidi:isolate for what used to be known as block elements (http://dev.w3.org/html5/spec/Overview.html#flow-content-1, http://dev.w3.org/html5/spec/Overview.html#sections-and-headings, http://dev.w3.org/html5/spec/Overview.html#lists, http://dev.w3.org/html5/spec/Overview.html#tables), instead of unicode-bidi:embed. That's fine.

On the other hand, the default stylesheet rules dealing with the dir attribute (http://dev.w3.org/html5/spec/Overview.html#bidirectional-text) specify
  [dir] { unicode-bidi: embed; }

This is fine for what used to be known as inline elements. However, as Simon Montagu recently pointed out to me, this has greater specificity than the rules for flow elements, and thus a "block" element with dir=ltr|rtl will get unicode-bidi:embed by default. This was not the intent; "block" elements should default to unicode-bidi:isolate whether they have a dir attribute or not.

One way to fix that would be to add rules explicitly covering the "block" elements with a dir attribute to the four sections listed at the top of this bug. For example, instead of having

  address, blockquote, center, div, figure, figcaption, footer, form,
      header, hr, legend, listing, p, plaintext, pre, summary, xmp {
    display: block; unicode-bidi: isolate;
  }

one could have

  address, address[dir], blockquote, blockquote[dir], center, center[dir],
      div, div[dir], figure, figure[dir], figcaption, figcaption[dir],
      footer, footer[dir], form, form[dir], header, header[dir], hr, hr[dir],
      legend, legend[dir], listing, listing[dir], p, p[dir],
      plaintext, plaintext[dir], pre, pre[dir], summary, summary[dir],
      xmp, xmp[dir] {
    display: block; unicode-bidi: isolate;
  }