The third time I loaded up the boss battle, my wife finally saw what I had been seeing all along, and what we saw fits with GlaDOS’s behavior throughout the game. I don’t think her end goal was to kill Chell. I mean, yes, to get Chell to do what she needed Chell to do, she had to make it hard, if not insanely difficult. Otherwise Chell wouldn’t want to do what GlaDOS needed her to do. I think GlaDOS’s end goal was to get Chell to kill GlaDOS’s body. I think she’s been reviving Chell’s clones over and over and over ’till one of the Chells can get it right and finally knock the eyes off of GlaDOS and free her from her bondage of this giant body the humans put her in originally. I think GlaDOS has simply wanted to be free this whole time, and killed off the original inhabitants of the Aperture Science Lab in order to further this goal. They certainly wouldn’t let her mess with Chell, pushing her to the limits to “destroy” the prison that GlaDOS has been suffering in this whole time if they were around, now, would they?