if you read the note Bill's "partner" left it gives a pretty good clue. There is also the magazine Elle steals

i just realized the magazine thing.... :O .... i thought by partner he meant... you know... buddy, friend or dude who has his back partner 

you are fucking awesome! i thought i was the only one

I did.  It was difficult to choose between her, Tess, Tommy, and Sarah.  Obviously there was no way in hell I could allow her to kill Ellie, but the mark of a great antagonist is when you can see their point of view even when you disagree with it.  Listen to her recordings--she absolutely reviles that life has forced her into this position, but when she had to choose between keeping Ellie alive or potentially saving the entire human race, you can see how many of us (not me, granted) would have made the same choice.  If you pay attention to the final conversation between Joel and Ellie, you can even see that Marlene was correct in saying that Ellie would have wanted to sacrifice herself for the cause, and that Joel just may be the selfish one here.

Storywise, Marlene took the final chapter of the game to an entirely new level.

Well I wouldn't say he is an antagonist. He is certainly not a hero, but a human being with serious problems, who hasn't been able to move on from the past and took the easy, selfish desicion regarding Ellie. I think he is rather real than evil, most people would have done what he did in his shoes.

Uhm, because he was Frank's boyfriend?