I don't think Pacquiao was a better fighter at that stage than what Hopkins was, despite him having accomplished more than Bernard and having more recognition. For what it's worth, I think the improvements that both fighters made post Jones/Morales are overstated.
Pac had already won 2 world titles, fought in multiple weightclasses and beat the likes of Sasakul, Ledwaba and Barrera and drew with Marquez. Pac was a proven world class and p4p fighter. Hopkins biggest success so far was going 12 rounds once and his best win was probably a man named Wayne Powell. Hopkins at the very best was a good prospect, perhaps a decent but unproven prospect. Judge for yourself.
morales over pacquiao is the greater win, especially now. they were both stars at the time of their trilogy. jones and hopkins were fighting for their first world title the first time they met. the first pac-morales fight is an all-time classic.
Morales over Pacman. Pacquiao was already proven and fought & beat Barrera like two years earlier. Jones beat a Hopkins not at his best and before he really became Bhop.
morales vs pac, easily. morales was in the twilight of his career and put up a great performance against a thriving pac.
morales over pacquiao. pacquiao was already a two-weight class lineal champ at the time he fought morales. plus he beat barrera who beat morales