I don't know about orphan train books, but I do know that there are a ton of WWII books being subbed, so I'll use that as an example. After a while, they all start to seem alike, even if the characters or situation are a bit different, it's still set in the time period, in the USA, with rationing and boys going off to war, and, and, and.
However, I have seen WWII books that manage to stand out from the pack by coming at it in an unusual way. The stand out books are usually very character driven so that you fall in love with the MC and get sucked into their life. There are other reasons too, more specific to particular stories, but they could be the POV the story is told in, or format or which character reveals the story, or where/when it takes place, or whatever you decide is the best way to tell the story.
So what makes the stand out books unusual? It's all subjective, but for me, the character and the part of the character's story that the author decided to tell, were what made them stand out. That and amazing writing.
You have to find a way to make it worth it for the publisher to put out yet another WWII or Orphan Train book. One place to start would be to go and read all the other books on your subject for children (yep, PBs, MG, and YA). Know what's already been covered and how. Then go back to your story and see if you can't find a new way to tell it that's unique and makes it jump out of the pack.
Good Luck!