Did you read the comics in question? The 05 go to the future and get into a fight with the Brotherhood there and come to blows with magneto himself when he arrives. Off screen this Brotherhood committed a horrible act (they stand in the middle of the city block they destroyed) the X-men are disgusted with with a large death toll and they worship Magneto like a cult leader. The Brotherhood in the future show up for more than one page, the two groups fight and argue. Calling every example I use a straw man isn't as compelling as you think, it tells me you have no argument to dispute the evidence.
If you want to actually understand who Wanda is, this isn't a bad request to consider, but we both know how you feel about her isn't about facts.
Edit: Had Magneto stopped being a super villain after the 90's even with all the acts he committed by then he'd still remain a huge super-villain in their roster. His legacy continues to get people killed when he goes into hiding with his followers. And he did all this without remorse, unlike Wanda. But somehow he's the hero and she's the villain.