Theory: Donkey Kong Jr's Biased Perspective

Abstract
Mario only seems evil in Donkey Kong Jr. due to the fact that we are seeing it from Donkey Kong Jr.'s perspective.

Arguments

 * Argument 1: Mario doesn't seem to act like this in any other games outside of Donkey Kong Jr., so this seems very out of place for him.


 * Argument 2: In Donkey Kong Jr.'s perspective, Mario is the enemy. Since Mario is taking his father away from him, it would make sense for Jr. to view Mario as a ruthless & evil kidnapper, probably just like how Mario views Bowser.


 * Argument 3: As seen with the Koopa Troop in Bowser's Minions, they view Mario as the villain even though to us, Bowser seems extremely evil. It's just based on who's perspective we are viewing the game from, and in Donkey Kong Jr., we see the game from Jr.'s perspective. If we were to see it from Mario's perspective, Jr. would probably be seen as the villain.


 * Argument 4: In later spin-off games (Mario Tennis & Mario Kart), Jr. and Mario seem to get along well. This would be because they aren't currently against eachother, so none of them would see eachother in a villainous way.