In the interview with the story team for Ralph Breaks the Internet, the sequel to Wreck it Ralph, there’s a few things that never made the cut. Just like the first film, no Mario in Ralph Breaks the Internet. As to why, story artist Jason Hand tells Inside the Magic that they couldn’t get the rights for the iconic game mascot.
Some of the stuff was that we don’t have rights to certain characters, because we’re working in a world of other people’s media. It’s like, that would have been really funny if we could have Mario [from Nintendo’s Super Mario games] in here doing this part, but it doesn’t end up working out because of that, and it’s fine and the story doesn’t actually end up needing it. But as individual bits, it’s like “That’s a great ‘Saturday Night Live’ bit!” Rich [Moore] and Phil [Johnston, the movie’s co-directors] are pretty much full of those things so it’s an endless amount of great ideas, honestly.
However, it appears Bowser will make a cameo appearance in the movie, along with a few others such as Sonic. As to why Nintendo wouldn’t let Mario in the movie? No one really knows but we can speculate that maybe there’s specific copyrights between Nintendo and Illumination Entertainment to only showcase Mario on the big screen with Illumination involved. Don’t hold your breath for any future Disney releases with Mario in it.
Source: Inside the Magic