I maintain Sabrina at the very least was at least implicitly somewhat tied to Rocket in canon. (Original Whip design, they took over her city, she defuncted the Fighting Gym, it was all very ominous. It likely wasn't a coincidence both the manga AND anime also portrayed her villainously.)
Blaine also, in recent years, has had his connection to Fuji and Mewtwo further established, and Giovanni's connection/acquisition of Mewtwo has also been canonized since USUM, so that anime story thread may also be sorta canon.
Then we have Malva, as you've already said - but if you're counting her we should also count Chairman Rose. While not a traditional villain, nor Gym Leader/E4, he was a public league official who ends up being a criminal you have to take down under region-threatening circumstances.
As
>>53651048 said, theres Piers and Marnie's connection to Yell, if you want to count the teenage hooligans who didn't really have an "evil" plan in mind with their trouble.
Then the theories about Geeta having more involvement with the events Area Zero than currently known. The newest game didn't really have any villains to speak of period, but you do get "badges" from Team Star, albiet this was a bit of a retread of Yell, which was a retread of Skull, so...
