He gained popularity when he got powers. She lost it.
She has always been superficially alluring. He is thoroughly magnetic.
He believes he can save everyone. She believes in him.
He would die to keep her safe. She would kill to protect him.
She uses her head. He makes decisions from the heart.
Lydia has always been defined by the men in her life. She's the queen of the school because of her sex appeal, she's popular because she's dating Jackson, and she finds her strength, and purpose, not in a romantic relationship, but in Scott. "Lydia would never run and hide" "Because of Stiles?" "Because of SCOTT"
Their steady friendship is so important to the show. Theo literally had to take her out because he knew he couldn't turn them against each other. They are one of the only boy-and-girl relationship in the show that doesn't end up dating because they don't need to be in love with each other to want to protect each other and keep each other safe.