Bookmarks discard window layout, scroll bar position, back/forward history, form contents, etc. They don't stay in sync with tabs so you have to delete and recreate them.
I kinda think there should be no distinction between tab and bookmark. Just give me tools to suspend old tabs into bookmarks.
I bookmark all tabs with CTRL-SHIFT-D then arrange the hierarchy manually in bookmark manager. Doesn't automatically do it all, but keeps me involved with my bookmark trees.
I wonder if you could serialize all that, and make a new "Enhanced Bookmark"
Actually, that would be a really cool directory service.