Like Sylar's feelings toward Elle, I have some doubts as to the extent of Elle's feelings toward him as well.
1. As many people have pointed out, s2, s3, and s3 flashback Elle differ drastically, so much so that it almost seems like she has mulipitble personalities or something. S2 Elle clearly displayed sociopathic and sadistic behavior. She saw absolutely nothing wrong with killing or causing someone pain, obviously enjoyed it on more then one occasion, and never cared about normal socially acceptable behavior. S3 Elle is shown to regret her past behavior to a certain extent, even the murderers and pain inflicted on others which she enjoyed so much before. She shows actual grief and anger over her father's death (however short-lived it may have been). Elle displays empathy for Sylar as well as Claire (to a lesser extent), doesn’t appear to want to kill others and only causes them the amount of pain that she seems to feel is appropriate for the situation (Lyle and Claire in the home invasion when her power was screwed up, not to mention harming Sandra the minimum amount when she and Sylar were trying to capture Claire). Heck, she even "evolves" so much that during the eclipse she cares more about Sylar's life then her own and even begs him not to give himself up to save her (which S2 Elle would never have done in either respect). The exception being of course in the car rental shop when she all but forces Sylar to kill the rental man. That she clearly enjoyed. Now flashback Elle on the other hand is not even of the same mold. She doesn’t want to kill others, doesn’t like seeing someone in pain, cares how her actions look to others, and even shows genuine remorse for tricking Gabriel into killing and causing Trevor's death. If they had kept either of these versions of Elle instead of swinging back and forth then any feelings she may have held for Sylar would have made a lot more sense.
2. As I mentioned before, it takes time to develop a meaningful relationship. Elle could not have developed true feelings for Sylar within one week. She may have held attraction toward him as well as a crush, and quite clearly guilt over turning him into a killer. She may even had been able to forgive him for killing her father, but anything beyond that including actual love? No. Her feelings may have been headed down that path, but as we all know they never had a chance of reaching that point.
3. Assuming that Elle was working for Arthur while she and Sylar were at Pinehurst, I think that Elle's relationship with her father would have played a large part in her behavior towards Sylar and any emotions that she may have faked towards him. No matter what you think about Elle, you can't deny that for her whole life Bob verbally abused her, neglected her emontially by withholding love and approval, physically abused her indirectly by forcing her power to harm her, as well as severally manipulated her. For me, all of this is evidence that Elle was abused by her father, and as often the case with those who have suffered abuse, they will often cling to their abuser and go to great lengths to attempt to please them. Elle's entire life has been built around trying to win Bob's love and approval (which is most likely one of the reasons why she was trying so hard to capture Sylar), and even though Elle appears to understand at times that this is an impossible feat she still keeps trying. After Bob's death that desire would still be there, which would have made it all to easy for Arthur too convince Elle to play Sylar. All he would have to do was say that it would have made Bob proud if she were to lie to her father's killer and fake affection for him, and Elle would have done so to the best of her ability regardless of her true feelings or if she actually wanted to or not.
I know that there are more issues that I have with Elle, but I seem to be blanking on them. Anyone want to offer up their thoughts?