They were one, the same. Mewtwo always regarded them as such. He was nothing but a shadow of Mew. He didn't mind, he was grateful to her after all. Without her, he wouldn't have realized how meaningful the world is or how wrong he was.
He found it unfair, however, when Mew's legend started to fade. As years past, no one could remember her story... nor did anyone seem to care. Instead, they sought to find the ultimate pokemon - him. The destruction he caused years prior started a new legend. One that replaced the new.
He sometimes wonders... does he actually deserve the attention? He was created /from/ Mew after, all. Mewtwo couldn't accept the fact that the story continued without the root.
Is Mew lonely? Having people forget about her, it must've been painful. She's a part of this tale, but was left unwritten.
Mewtwo felt guilty, having to steal the recognition Mew deserved. But when he saw a carefree smile on the other's face, he found he couldn't care less.
She was happy.
Because he was right there with her.