I think we take it for granted that Wario has always been this way. He is not an evil clone of Mario. He is not like a guy who deliberately styled himself to be a fucked up vile Mario after being wronged by him. Wario is not a Metal Sonic situation, where he was built mockingly to usurp the original Mario, nor did Bowser's grandpa see a prophetic mural of Mario with a Fire Flower fighting to protect the Master Emerald and subsequently choose to design the Ultimate Lifeform in the image of this protector. My point is, there's no Wario origin story. Wario was Born.
We have SEEN Baby Wario. He's been a DOCTOR, even. He came out of the womb - which in the Mario universe is a stork's bag - fully, already LIKE this. Wario is the way he is because the forces of nature just had it out for this one baby. His parents NAMED him Wario. At best, maybe Wario's parents had a vendetta against Mario's parents and asked the stork for a baby who could utterly fuck up Mario. But, there's a good chance it's just a bizarre, cosmic coincidence that Wario is an upside-down Mario.
You can't make any creepypastas about the dark truth about Wario or whatever, because the facts as presented are so plain... and yet so much more interesting. This is pure conjecture on my part, but it is plausible that Wario did not remember their baby encounters. He could have seen Mario on TV one day and realized, "wait, I have to be the evil version of this guy," and inserted himself into his life from then on. My point is, it doesn't matter when it started between them. There's no vendetta. Just a purpose.
And do keep in mind that Waluigi is, apparently, NOT Wario's brother. They are, according to Charles Martinet, "two nice, evil guys who found each other." This is the only thing anyone who works on the series has ever said on the subject, and I feel like I trust Charles Martinet more than I'd trust anyone else on this one, single particular piece of information.
Frankly, I think in the context of all of this, that is so much more beautiful. Imagine you are Wario, and you realize you're the evil version of Mario and you start fucking up his life, and don't get me wrong, it's good. Wario is nothing if not vivacious. But Mario, famously, has a brother. Mario's whole thing is that he is a brother. Wario has no one. He's just an anomaly.
Then imagine, one day, you're Wario, you show up to play some tennis, right? You're probably like, "well, maybe I can find a Koopa or something as my doubles partner." And imagine you see this gangly fucked up purple man walking around looking for a partner. You lock eyes. And you realize, this is the brother your parents couldn't give you. Only destiny could give him to you. And now, with him, you're complete. You can finally be your full self. It's not like life was bad alone, but it all makes sense now. Together, you can finally, truly achieve what you were made to do. No one can understand why the forces that be gave you this mission but you'll both be damned if you don't give it everything you've got.
And look, I can't stop you from shipping Wario and Waluigi. But in my opinion? What they have is deeper than family and it's deeper than romance. I don't think any of us can understand what Wario and Waluigi have, unless you were born an only child as an evil version of a guy whose most famous attribute is having a brother and you meet an unrelated evil version of that brother who is also an only child. Which, hey, there's a lot of freaks on this site, maybe you have gone through this, actually.
If that is the case - then shoutouts to all the nice, evil guys who found each other.
Hire me to make Mario Movie 2.
According to comics based on the Mario games, Wario did know Mario as a child, and was always annoyed by Mario's general Marioness. Then again, these same comics have Wario making a deal with the devil, so.... take it how you will.
I'd post images, but for reasons beyond my comprehension, I cannot. So here's a couple of links.
Like you said, no need for any fan theories, the truth is more fun.
