I'm one of the people who likes Nunge over Pemsl, long term. There's three reasons:
1. You are correct that Pemsl has been the better player thus far; however, I didn't see much progress in Pemsl between his freshman and sophomore seasons. In particular, he remains extremely left-hand dominant, to the point where teams overplayed him in that direction his sophomore year and largely negated his ability to win one on one matchups in the post. His shooting percentages didn't change much, IIRC, but I remember him often not even trying to score when he got the ball in the post his sophomore year, even when he was not being double teamed. If we are going to make a concerted effort to get the ball into the post, then the post needs to either (A) draw a double team and find an open shooter/cutter or (B) shoot and score if he isn't being double teamed. I saw Pemsl get shut down by single coverage way too often for my liking as a sophomore whereas he often defeated single coverage as a freshman. I didn't track it, though, so it could be my own perception/biases. My worry is that Pemsl has plateaued.
2. Nunge has a promising outside shot. Having a PF/C that can shoot threes is a big deal for offensive spacing. When Cook and Garza were in the game together, only one of them (usually Garza) would be in the lane at any given time while the other would be out on the perimeter. The other team would not guard that player very closely, though, and instead would keep an extra defender in the lane which makes it harder for our other post. If Cook and/or Garza could magically hit 40% of their threes, then our offense would have been a nightmare for opposing teams (although it was still very good). The really good Wisconsin teams at the end of Bo Ryan's tenure had bigs that could shoot the ball. Obviously, we all know about Dekker and Kaminsky but before that it was Jon Leuer and Keaton Nankivil who also had solid outside shots. Bigs that can shoot help out a LOT.
3. Nunge's height gives him more potential as a rim protector and more ability to play center. Pemsl has quick feet and we all just saw Virginia win a national title with 6'7-6'8 forwards that can switch everything so I am growing higher on Pemsl's defensive value. But Nunge has decent feet, too. He might not be quick enough to play the SF spot but I think he has a ton of potential as a future PF/C.
I'm not trying to be super down on Pemsl. I love his strength and his quick feet but I am disturbed by the lack of development with his right hand. I am also very intrigued by Nunge's size and outside shooting ability so I think he has the higher ceiling.