Hah! I've not done one, but two Pokemon adaptations of books I've read: "Old Man and the Sea" and "Da Vinci Code". I'm more known having adpated "Da Vinci Code," so I'm going to talk about that.
The first part of the plot of "Nothing, Everything" (the fic that's based off of "Da Vinci Code") is almost the same: one person gets wrongly accused but another person helps her out. At the same time, both found some clues left behind. The second part of NE though is where I put my own twists to it.
Another thing I did is the theme. "Da Vinci Code" has the theme of religion, but "Nothing, Everything" has the time of history, basically the concept of "history repeats itself."
Last thing is the characters. The characters in "Da Vinci Code" are totally different from "Nothing, Everything" (although one of them is slightly based off of one of the Da Vinci characters, but I still managed to make him my own).
I admit, at first I was having a little trobule making a Pokemon version of "Da Vinci Code." Heck, because of that I almost quit on it. The original version of "Nothing, Everything" is basically almost like that book. However, I then decided to try it again and I basically rewrite almost everything in order for that to happen.
All of that has paid off as I've been getting reviews that they like my own adpatation of the book. Heck, one reviewer said my version is better than "Da Vinci Code." XD;
So yeah, Pokemon/any other fandom adaptations of books can work as long as you put a few twists on your own.