I believe Noxus is pretty misinterpreted as the "Bad guy" city state in LOL lore. Sure, it doesn't have Demacia's commitment to Justice, Ionia's belief in balance or Piltover's pursuit of progress, but it is by no means evil. Its inhabitants just believe in a philosophy embodying survival of the fittest, which is pretty harsh but not actually evil. In fact many of the champs from Noxus (like Katarina, Darius, Riven and Talon) aren't necessarily evil; they're just either ruthless or dedicated to the Noxian cause. IMO LeBlanc or Vladimir could be the closest to "Villains" in a general sense (LeBlanc uses her illusions to manipulate politics and stuff, Vlad enjoys killling people just cause he likes seeing and controlling Blood), but i think Non-noxians Lissandra, Zed, Mordekaiser, Cho'Gath, Brand and Thresh are worse villains than these guys (Thresh and Mordekaiser steal souls and torture them; Zed killed Shen's dad just cause he wanted to use forbidden techniques; Lissandra, Brand and Cho'Gath just wanna end the world)
Zaun, on the other hand, is a bit of a madhouse (Save for Zac and Blitzcrank...and possibly Viktor if one reads his backstory)
Yeah. Shen's dad was a jerk to Zed, singling him out and treating him as inferior to his son. Even in the end, he tricked Zed and tried to kill him feigning peaceful intentions, to which Zed accepted. I think the true villain was the previous Eye of the Twilight.