I may have misunderstood what you meant, but copy and paste in tmux works in vertical panes just the same as horizontal panes: http://d.pr/i/93p2/wNHyqVFr (copied from the right shell into vim in the left).
I too generally use tmux's built-in text-selection and clipboard when I'm copying from pane to pane, because it's more convenient.
Or do the rotation thing. Or do the copy-mode thing. More than one way to skin this cat; just depends on which workflow you wish to adopt.