I had a different hunch, and I guess neither of us will ever know for sure, but I stated my hunch back in April, and at least in its outline it came true:
My hunch is that Pope knew his personality and Stoke's would never mesh, and that having him on Kentucky's team as the Big Dog was likely going to be a disastrous clash of wills. While he couldn't just say no thanks to the guy, he wasn't all in emotionally with that recruitment.
I think Pope had his eye on Momcilovic all along, knowing there was a risk the guy would stay in the NBA draft, but not much of one. After all, he's being paid at a level he'd never have attained late in the first round. With the money saved on Stokes, AND with Kentucky's cachet, a wide open slot as Top Dog and his 3-oriented offense, I think Pope knew he had the best shot at Momcilovic if he stayed in college, which was likely.
My hunch makes more sense if you are Pope and know this is a make or break year: Do you want that resting on the shoulders of an egomanic narcissist like Stokes or a guy like Milan? No question in my mind.