I think a lot of people are limited by what Stefan says to Lexi in 1x08:
Stefan: Katherine and Elena may look the same on the outside but on the inside they are completely different.
Lexi: So Elena is not a raging Bitch then, huh?
Stefan: No. Elena is … Elena’s warm and she’s…she’s kind, and she’s caring, and she’s selfless
I won’t disagree that Katherine and Elena are different because they are in that Katherine is most of the time selfish while Elena is most of the time selfless but they aren’t completely different and what Stefan describes Elena as isn’t all that she is. There is an overlap between them and that is their Petrova fire. Stefan has been harping on how Elena is the opposite of everything Katherine was which has never been the case as Damon has noted that she has got spunk, she is feisty when she is mad and that she can be manipulative when she wants but for most part she became reserved as a result of her parents’ accident because she blamed herself for going to that party due to which they had to pick her up and there were only windows when you would see her pre-accident self or her fire which only Damon recognized when others thought it to be gone. Stefan tells Caroline in 4x03:
You grew into yourself when you became a vampire. You changed and Elena is changing too
This is who Elena really is and that girl has always been lurking inside her even after the accident but she repressed her because of the guilt but by becoming a vampire she can’t do that anymore and so now she is more of herself than she was before and it’s just that Stefan never really noticed and that is a big part of why a large part of the audience was fooled too. Instead of looking at it from Stefan’s eyes if they had just paid attention, they would have seen that there was always more to Elena Gilbert than meets the eye.