I can understand being confused by emacs' undo but I don't understand what copy-pasting has to do with it. If you undo too much then you can effectively "re-do" by stopping your undo sequence (simply moving the cursor around for instance) and then undo your undoing?

A big advantage of emacs' tree-like undo is that you never lose any part of your history unlike a naive linear undo sequence. Like in this Firefox edit box for instance, if I type a word, undo it then type an other word I can't go back to the state I was in before I undid the first word. With Emacs I can usually restore any previous state my buffer was in (within the limits of the size of the undo buffer that is).