I'd say chances aren't bad for it. The two companies have teamed up to promote both Minecraft and the ability to play certain games together on their respective consoles to the extent that an XBox is shown, in a positive light, on a recent Nintendo ad. On social media, the two companies were acting buddy-buddy a month or two back, so it looks like the relationship between them isn't as antagonistic as with Sony.
As mentioned before, Phil Spencer had supported the idea of including Banjo in Smash 4, which while didn't come to fruition, does show that someone up on Microsoft's ladder is open to the idea of sharing their characters. In addition, in Minecraft, skins of several MS characters such as Banjo, Master Chief, Joanna Dark and Marcus Fenix are all available to play as on the Switch version, again showing the company is fine with their IPs making some form of appearance on Nintendo's console.
Then you have fan demand, which has been wishing for Banjo to show up in Smash since Melee. I believe the ballot support for the character is rather high and most certainly on Sakurai's radar. In addition, Minecraft is one of the largest games of recent times and certainly would appeal to the newer generation of gamers, so I would imagine that it would be well recieved if included in Smash as well.
At the end of the day, Sakurai gets the final call and it'll be up to him to determine which characters make the final cut. He has pulled several hefty strings to get even less-likely characters like Cloud, or Snake in Brawl, in, so if he desires, he'll have no trouble working his magic with any company he contacts.