For a superhero flick that tries to be very nontraditional, Deadpool wraps its ending up in a neat little bow.
Deadpool beats the bad guy and gets the girl. Vanessa may be mad at him for letting her think he's been dead this whole time (whoops!), but that fades in an instant, and soon she's in Deadpool's arms.
There's also a callback to an earlier joke in the film. When Wade and Vanessa argue about his desire for her to leave before his cancer gets bad, he tells her that he's going to boom box Wham's "Careless Whisper" outside her window in the next life. Vanessa's not having it. She doesn't want to think about '80s slow jams in the next life; she wants to focus on Wade's life right now and, more specifically, how to prolong it. At the end of the film, as Deadpool and Vanessa make out amidst the ruins of the shipyard and the camera zooms out, he blasts "Careless Whisper" off his smart phone.
You can look at this callback two ways. On one hand, it suggests that after so much turmoil, Deadpool and Vanessa have fallen right back into their own ball-busting version of romance, and everything's going to be okay. On the other hand, it might also suggest that these two lovers are actually in the next life. Not literally; they're not in the afterlife or anything like that. Rather, now that Wade has a new job as Deadpool, the Merc with a Mouth, their lives are going to be completely different than they were the first time around, and not just because without his mask, Wade looks like a giant dried salami.
Sorry, Wade. There's just no other way around it.