Mutants like Deadpool, Colossus, and Negasonic Teenage Warhead aren't just men and women with extraordinary abilities; they're symbolic of marginalized and oppressed peoples. Just like women, racial and ethnic minorities, the disabled, and the LGBTQ community, Deadpool and his fellow mutants have to fight to fit in and be accepted for who they are.
After Deadpool's mutant DNA is released, he also struggles to accept himself. The change in his appearance is drastic, but it also comes with super-powers and cures his cancer. In other words, he's got a lot going for him. Ideally, he should focus on the big picture, but that's far easier said than done when you're noticeably different. When he walks down the street, people stare and murmur to one another. Ultimately, Deadpool's insecurities rob him of valuable time with Vanessa.
At the end of the film, Deadpool lefts Vanessa lift his mask, essentially coming out to her, and he's relieved to find that she loves him all the same. She doesn't love him despite the fact that he's a mutant; she loves him because he's a mutant. He's just Wade, and she loves everything about him.
Okay, maybe not his devotion to Wham, but she loves everything else.