Boss themes are close, but Gandrayda gets the edge. Gandrayda also spawned the Sammy nickname, for what it's worth. But the real clincher is just the fact that when Dark Samus pulls out her version of Samus' weapons, they are superior (and cooler looking) than Gandrayda's.
I like Rundas but GLaDOS is a bit cooler. I also would kinda like to see a finale with characters from three different series instead of one PvZ and two Metroids.