The reason the WFT hasn't replaced anyone is because there's no such thing as "slots." Let's say Snake is cut. Does that mean WFT replaced him? Or Megaman? Or Pac-Man? Or another Konami rep? People would say the Konami rep, because it'd be convenient for them to use as an argument against the Konami rep.
If R.O.B was removed, people would automatically assume it was the WFT's fault, or another retro character's fault. If Mr. Game and Watch gets in but not R.O.B, using that assumption, it's just as much fault of Mr. Game and Watch as it is of the WFT. Same goes with Waluigi. Is it Rosalina's fault Waluigi isn't it? No. Saying that Rosalina made Waluigi not in the game is something done because it's convenient fuel to flame Rosalina's inclusion.
What about a character like Isaac? If he's not in, who's fault is it? Another character who gets to represent their series? Maybe it's Lucina's fault, because she's the reason everyone's not in. Using that logic, Lucina stopped Skull Kid, Ashley, Anna, Tharja, Blood Falcon, Sukapon, Diskun, Talonflame, and any character you can think of from getting in.
The reason people say one character replaced another is because it's easy to say that. Nothing more.