Agree with you on the suitcase perhaps getting too much attention because of the LS intruder theory. Also, remembering that FW said he "moved it" when looking for glass, could mean it was no where near the window when FW grabbed it to move it, which might mean it was tucked out of the way in the train room - along with a lot of other junk that was stored in there.
However, in considering that the suitcase and it's contents might be connected, since LE is guarding the name of the book and CBI's report of fibers on JB's shirt, I highlighted above the points that you made which lead me to think there might have been an intent to ditch the suitcase. If that book has incriminating evidence on it, and a lone parent had intended to try to fool the police and the other parent into believing JB was kidnapped, then I think it is possible the suitcase would have been taken out of the house with her.
Actually, I did consider the book might have initially been put with JB's body, as part of her "comfort package", and moved out at the last minute by a perp who might have worried about prints or something else being discovered on the book. If a title is being withheld by LE, isn't it possible some other detail about the condition of the book is also being withheld?
Patsy gave a statement to Haney that she didn't know that JAR had a Seuss book in the suitcase. Of course, Patsy has been accused of other lies. And, we cannot rule out the fact that JAR might have had the book in there, without getting him on a witness stand or in a GJ interview.
Your statement about the college boy using a blanket and pillow rang so true - so much that for a moment I had to ask myself, why on earth would JAR have even had a DUVET and SHAM on his college dorm bed to begin with. Come on, a college BOY with a SHAM???
OK - all you guys who had Shams on your dorm bed, chime in, please! Or I am going to start wondering if that duvet and sham actually came home from the dorm!