As far as I know, anytime a game pairs characters together, these two are one of those pairs. To be fair, pairing systems are kinda rare in the spin-offs, especially factoring in Kart and Party. However, I don't think that's enough to say that they aren't related at all, just that the relationship isn't explored most of the time because the characters only appear in spin-offs that don't care to explore anyone's relationship with anyone.
Also considering his design is so similar to Wario that retconning their relationship to him being a random, unaffiliated guy who just so happens to look like Wario, but otherwise has nothing to do with him. I could definitely see him only getting along with Wario during team games and adopting an "every man for himself" mindset in everything else though.
It's not a retcon. Their entire relationship is "they're just a guy who plays together in sports and both enjoy being underhanded." That's actually what happens.
Party has pairings actually for a small chunk of games, and even then, they're just team names. Wario and Waluigi are just one of many and it's not specialized or emphasized that it matters. Double Dash is their only notable one that isn't just regular Sports(naturally Soccer doesn't bother with this, but that's cause they're both Captains. Of course they can't team up in the gameplay itself).
This is what I meant by people overstating their partnership too. It's a small thing meant for the Sports games that is given little attention outside of it(Party slightly acknowledges it, but it's not an important thing to them. Everybody can team up anyway. Kart is still a Sport, as is Olympics, so they don't count as standing out either). That's also why there is no retcon. Waluigi was originally envisioned as Wario's brother, but that was a thought that was never actually brought to fruition. I might've typed that poorly in the earlier post, though, so apologies for that.
To be fair, he doesn't ever actually cheat in the sports gameplay, and it kinda makes sense to nix the idea if you aren't ever going to follow through with it (because it would break the game if they did).
It's just a fun cutscene thing anyway. No reason to get rid of it. It's about showing his personality. And as said, it would break the game if it did. The thing is, it shouldn't matter anyway if these are cutscene things made to flesh out a character or not. Applying everything to gameplay is bad design. You can have both separated fine without any issues.
I'd also say it's another reason why he should be in literally any game that has room to flesh him out. What little characterization he has beyond "very kooky, attention hungry, and kind of a loser" entirely depends on the game's vibe and mechanics.
And a suave person, who doesn't mind underhanded tactics, has a crush on Daisy, isn't adverse to teaming up with anyone(in competitive sports only). He also represents Mischief in Mario Party 3, so even then they have a clear defining point for who he is. He has more than is being given credit for. It's just that this is Mario, where they aren't going to have big stories often outside of the RPG's(usually in those. Paper Mario had two games with some far lesser stories than the rest of it). There's nowhere to properly flesh him out(as he was simply created for Sports stuff, and isn't really privy to other genres much beyond some fun competition very often). DDR was as close to a unique genre as he ever got, and it actually fit his personality well within the story. He's not greedy either, which is a fairly key theme to WarioWare(everybody is in it for the money to begin with. That's the purpose behind it). So throwing him in just cause it has some kind of competition doesn't make much sense on it alone. If he was first introduced in Mario Party, that'd be one thing. He'd be built more around the idea of various mini-games. But he wasn't.
Overall, he's kept to an area that emphasizes his characterization. That makes sense. He has enough personality that he's not some boring or blank slate character. He's more defined than some wish they were. You know who he is. He doesn't need to appear in Wario's games to be already quite fun and interesting. It's why he's already a very popular character. He's already iconic with what he has. Besides that, when he got a game where he was the starter villain and he's not actually involved with Wario specifically? ...That says a lot. He doesn't revolve around Wario only. It also shows quite well that their "teaming up' is context-dependent. Which is the point I'm making; that their relationship is very specific and isn't "everywhere" either. So why isn't Waluigi involved with Wario more in the Wario games(or at all present in the games beyond a mention)? Cause he doesn't only revolve around Wario and people are ultimately putting them more together than they really are to justify it.
I'm all for fleshing him out, but I'm not going to pretend he's a missing thing in WarioWare either. They can focus on Waluigi as a character and not involve Wario just fine to justify it too. They already did in the DDR game, after all. Yes, he was created to be partially involved with Wario(in Sports, generally). No, it's not his only defining aspect either.