Wanda's OP powers, Agatha's seemingly OP powers, and Wanda/Vision's kids powers, having them as Mutants would make them/Mutants unique, and change the status quo forever in the MCU.

Like instead of having it where they got their powers from an experiment, or was taught to use magic like Doctor Strange, they can have it where they was born with it thru the lament X-gene, and after they came in contact with the Gems/Stones it unlock their powers.

Also with the mention of the Nexus which seems to have something do with the Multiverse in the comics, if Agatha and Wanda can have access to the Multiverse then making them Mutants would make Mutants even more unique in the MCU.

Another thing it seems MCU Agatha already different with her seemingly being Wanda's villain than mentor.

Also right before she revealed her true ID to Wanda, she told her you didn't think you was the only magical girl in town did you? Then after she revealed her ID to her she told her nice to finally meet you, then she used her magic on Wanda, and showed her it was her pulling all the evil strings all along.

Now there's two episodes left to reveal why Agatha is doing all this, and I just think maybe it'll have something to do with Magneto, Mutants, etc. etc. for Disney/Marvel to use as a last minute twist so they can say surprise! Bet ya didn't see that coming did ya fans?