I voted for Cassandra a few days back but hadn't gotten around to justifying my choice yet. So here I go!
It's obvious that Cassandra never could have done something as huge as destroying the universe or something hyperbolic like that. That's fine by me, though. We can leave the over ambitiousness and over powered ness to the likes of The Master and Davros for group A and the Black Guardian in group B. It's nice to have re-occurring villains.
Her nature and origin is unique. She's the last human being in existence. This is a pretty freaky idea in of itself as the thought of my own species going extinct makes me a little queasy, even if it is billions/millions/thousands of years n the future. Then we get the fact that Cassandra is just a sheet of human skin pulled out like a squarish trampoline. No hands, no arms, no legs, no feet. Veins and a face. It's grotesque in thought.
Once we get beyond the physical nature of Cassandra we have to deal with the fact that all of those nasty elements of human nature we prefer to brush under the carpet are pretty much the only elements left. Greed? Disregard for life other than oneself? Egotism? Arrogance? Elitism? Vanity? I'd like to think that given such a huge period of time that we'd be able to shed at least one or two of those things. The vanity has also reached absurd proportions with all of the work she has to do to both keep herself alive and looking good. We went from desiring face lifts to being face-lifts.
I will concede, though, that the overall execution of her character was a touch flawed -- especially in her second appearance. The mind-swapping thing was handled too flippantly to be taken too seriously. If they would have explained that power by the Doctor having a line like "Oh, yes -- in a billion years time humanity has a complete understanding of what you might call 'the human spirit is' and can even manipulate it with technology." But no. We got hi-jinx. Also, while I thought that her death was perfect for her character, I do wish we would have gotten one or two more appearances out of her before she bit the dust. Imagine if she appeared once a season and then died in Season Four -- the fans would lose a villain they'd come to expect for the last three and a half years.
And that's all I got to say about that.