...Wasn't it like two poor fans who took it too seriously and that was it?
That isn't going to mean much. Reggie did talk to Nintendo about Waluigi after seeing the massive outcry.
It makes sense. He's been massively popular for ages. Of course there was going to be fan outcry. There was for Isaac too(but apparently Nintendo nor Sakurai knew how big of a deal it was to get him playable. He can't hold a water to how well known Waluigi already is as playable, since even Sakurai acknowledges that him being playable wasn't in the cards all the way back in 4. It doesn't seem like much, but he doesn't talk about anyone else specifically like that. He speaks of AT's who couldn't be playable "at the time" so had this role instead. In addition, he never talked about this after DLC was a thing. If Sakurai is 100% in charge of DLC, he could plan purely around base roster and gameplay roles when choosing who is who. But... he isn't anymore. He has solely the power to veto, and "He's an AT!" is not exactly a strong argument anymore. It died the second base game roles were shifted with Min MIn(and somewhat was weakened with Trophies getting a playable role in 4, despite being Veterans. It shows that Sakurai... doesn't care all that much. And unlike last time, Mewtwo was both a Trophy and planned playable despite this. These in-game roles are way overstated on how important they are. And the other big thing is that he's not the only one to choose these. He has a team that helps him. A cut AT doesn't make them magically more likely, for instance. Sometimes it goes that way, but that's for other reasons. Dark Samus got in because of Echo and popularity. The AT got cut because she was chosen to be playable. This was decided by base game. The second DLC comes around, things change as needed).
Nintendo might not choose him, but they aren't going to care about the AT. Don't kid yourselves. It has jack-all to do with businesses. If Sakurai's going to say no, it's cause he can't figure out a good moveset. He is not going to avoid it because of the AT when A) He can disable it or B) He can ignore it.
The only time those roles would've mattered at most is trying to figure out DLC right away. ...And Nintendo controlled all of it anyway(PP doesn't count, as it was made DLC after base game was decided but still with base game in mind), so Sakurai may have veto'd some ideas for Pass 1 possibly. Sure. He might've already figured this was the only DLC and was satisfied with their roles at that time. Pass 2? If he did, we wouldn't have seen Min Min, who breaks the same fan rule "already a base game role that affects gameplay". AT's aren't actually different in that regard. He already makes them unable to appear in countless matches, picking and choosing.
If Waluigi isn't getting in, it's moveset issues(specifically unable to figure out how to make him dance in his head), Nintendo not suggesting him, or some kind of weird issue in that Sakurai can't do enough of what he wants(similar to moveset issues, but more than he can't use the animations he wants cause of "how they're represented" is still a thing to IP holders. Understandably so. If Sakurai doesn't own the character, he's limited). ...Albeit, I don't see the third thing being remotely likely, but the other two are reasonable possibilities. The third thing applies for 3rd parties generally, though. Pokemon included(which, well, isn't straight-out first party either).