Because:
1. Her dad died
2. her power was hurting really bad
3. Sylar killed her

i always felt bad for her because you knew how screwed up she was and how cruel her dad was to her but i think in season 3 terrible things happened to her. bob was still telling her how much of a dissapointment she was, bob was then killed by sylar, she was almost killed by sylar shortly after,she had the guilt of letting go all the level 5 villains, she got fired from the company and was left with nowhere to go, her power went out of control leaving her with unbearable pain, we found out about what she had to do to sylar and that she really did like him but had to follow orders, she was shot in the leg, her boyfriend (gabriel) was killed right in front of her, and then of course she was brutally murdered... poor elle :'(
but season 2 was rough as well when she had to learn about her past and how shed just dissapoint her dad and of course she got shot.

She was more human in season 3. Plus, she had her head cut open.

I have felt sorry for elle through the whole thing, bless her! She didnt really have the best life, did she?! :) but i think season 3 was definatly worse. For all the reasons chels125843 said.
:) x x

She was killed by the man she loved.

Her father was killed and she found his body, plus he'd been killed by Sylar so she probably blamed herself for his death since she'd failed to capture Sylar previously. Then Sylar attacked and nearly killed her. Then her self-defensive electrical outburst caused loads of prisoners to escape, and she was fired. Then she can't control her power and keeps electrocuting herself. Then she gets into a relationship with Sylar/Gabriel only to have him sacrifice himself for her. Then he loses control of his ability and kills her....

That's a lot worse than S2. The events in S2 weren't really that bad for her - you just felt pity for her for what she'd revealed of her previous life.