I've always imagined that he didn't do NEWT level potions, purely because he would have needed an O at OWL level. In my fic, he dropped it because he couldn't stand Snape. Tonks, however, took it at NEWT because she was a hard worker and bright enough to get the necessary OWL result.
Charlie Weasley was also Quidditch captain as well as a prefect. Percy describes him as an outdoors type. He doesn't strike me as fantastically academic, and Dumbledore didn't choose prefects on their academic ability.
We don't know enough about Charlie, though, so you can go either way.