Two things of note happen at the ending of The Host. In the final chapter before the epilogue, Wanderer is removed from Melanie and implanted in a new body. The big-picture scenario here is that the roles are now reversed. The humans are now the body snatchers, taking the aliens away from their community and blasting them into outer space.
Think back to what we know about the alien invasion: humans were picked off one-by-one, in small groups, until the aliens had taken over. Now, the aliens have their own society, their own jobs, friends, and families. And the humans are doing basically the same thing: taking the aliens away from their mates. While they aren't killing the aliens, they're basically ensuring that they'll never see their friends and family again by putting them on a rocket bound light-years away.
Hm, there really isn't much difference between the humans and the aliens any more, is there?
On a smaller, but no less important, scale: Melanie is reborn, hooray! And Wanda doesn't have to die! Double hooray! But now she's in a sixteen-year-old body of a girl who looks like a real-life kewpie doll. Huzza-wha?
Throughout the novel, Wanda is insecure about her maturity level. She's been on the planet Earth for just around a year and she's still not totally in control of her emotions. "I feel like a child all the time," (25.108) she laments. At times, she feels trapped by Melanie's overwhelming emotional reactions. "I started to cry again, like a child, afraid that I would never get free" (30.18).
So, what do they do when they find a new body for Wanda? They replace Melanie—strong, athletic, tall, early-twenties—with a short, sickeningly cute, weak, living doll of a child. This is not only insensitive to Wanda's feelings, but it's more than a little controlling. Athletic Melanie is a threat. Fragile little girl who gets treated like a child is basically property. At least they still get to utilize her best talent: shopping! Her shopping ability is enhanced by her unassuming cuteness.
On top of that, Ian is almost thirty years old. Wanda's new body is half his age. Do we even need to expand on how creepy that is?
In the epilogue, the tribe of humans meets another tribe of humans in the desert. This changes their world. There are more survivors! Not only that, but they have a sympathetic alien, named Burns, in their entourage as well. Like Wanda, they kind of use Burns as a slave to do their bidding, but he seems fine with it.
By this point, the caves are home to both Wanda and Sunny, both aliens happy to co-exist with the humans. By meeting Burns, Wanda realizes that she's not that unusual after all.
And this encounter raises a few questions: Will the human factions get along? Will the aliens always be content with their submissive co-existence? And who gets dibs on all the Cheetos?