The issue is that GLaDOS is rather iconic by this point in nerd culture, so having her reprise the same voice for another random AI, I just feel that takes away from the movie more then it adds to it. Now anytime the AI talks all the nerds are going to be like "Haha it's GLADOS!" rather then paying attention to whats happening, then half-way through the movie after not hearing a single snarky line and just a bunch of "powering up suit reactors", people are going to be like "Why isn't she acting like GLADOS?"
Again, it's like how Blizzard recently got Jim Cummings to voice a character in WoW, Lorewalker Cho. They didn't just decide "Well, Pandaren are technically bears, so just do the Winnie the Poo voice.", they had him do a different voice.
Again, I would be fine if Ellen was talking normally and only through certain points spoke like GLaDOS to elicit a nerdgasm, but they instead decided "Well you are a computer, so just be GLaDOS."