Since you believed Brain is the main antagonist of the cartoon,Animaniacs,but I don't think Brain is the antagonist since Animaniacs is a animated cartoon variety show and has no regular main antagonist,but has their own antagonists in their own skits such as the Warners' having Plotz and Ralph,as well as facing off and annoying other foes such as Dictator Umlatt. Brain is no antagonist,but more as a legit failure,but determined hero protagonist in the vein of Don Quixote in the original 90's show and Pinky and The Brain. While he seemed like a villian,but he was nowhere near as evil as he was in the 2020 reboot. The time the Warners and Pinky and The Brain ever interacted were Sir Yaksalot and Wakko's Wish(which they gave Brain some political power by making him trusted advisior),so I think The Warners weren't the arch-nemesis of the mice,since they're more like co-stars and off-screen friends/partners. Through despite his ego and ambitions, he has a moral consicence for his actions and his abuse of Pinky wa justified since it was done through annoyance and intolerance. While he did have a vicious streak in the original Animaniacs episodes,it was soon toned down when the two ambitious mice got their own spinoff and Brain was given more sympathic traits and shown to be friendly to some people,despite acting superior and conseneding at times.
I think the 2020 reboot is when The Brain truely became a legitimely evil mastermind since years of not succeeding his lifelong goal of world domination finally drove him over the edge and made him lost his sanity,causing him to take his plans to more diabolical,heartless extremes and his abuse of Pinky has leveled up a bit since Brain now tends to take joy out of insulting and abusing him so much. Some of his more edgier and ruthless acts in the reboot is that despite succeeding his goal of world domination when in his evil plan to become a popular meme resulted in Pinky's video making him a popular phenomonon,he was still outright evil when he told Pinky that people would finally view him as internetmeme/dictatorforlife before Pinky ruined it by messing with his mind-control filter,posed as a senator by blackmailing every senator in the senate until he is the only one left,he and Pinky almost sabotaged a spaceship in order to go to space when none of the aliens didn't want to take over the world like he wants(complete with a evil laugh),attempted child labor to build bombs,and his most evil act in the reboot is that he tortured his genitically-enchanced wife,Julia when she was shown to a moral compass compared to Brain's meglomanical,evil nature and wanted to help the world instead of taking it over like what he wants,which resulted in Brain placing a chip in Julia's head to mind-control her to get him to take over the world,which it malfunctioned,sabotaging her chance of being elected president and driving her crazy. I know Brain wasn't as evil in the 90's shows and more justified in his plans and had sympathic traits,but the 2020 reboot really made him a cruel,ruthless mastermind desperate for world domination and left in hopeless frustration after so many failures in his plans and goals for 27 Years
. I hope in Season 2,Julia would get revenge on Brain by forming a angry mob against him or defending the world from him or Pinky would point out how more evil Brain has become since he started his plan 22 years prior and tell him to make amends and try to be a good person. I feel like Brain has become the Stewie Griffin/Invader Zim of the 2020 Animaniacs reboot instead of a rodent version of Napoleon in the 90's cartoons and I appreciate the writers of the reboot what they're going for by making Brain more antagonistic and edgier.