That sounds pretty neat for Deoxys. Ideally, they may push someone from Pokken for the NX version or whatever the new hottest Pokemon is at the time of release, just planning that particular Pokemon in advance. I mean, developers share stuff they're working on all the time. That's how Greninja got in, after all(I don't mean cause he was new and hot, but because of developers sharing plans).
Anyway, I read Push's current articles on this idea. Sakurai does not like straight ports. If he is involved, it's likely going to be a bigger game, but less likely to have more players. If he's not involved, and it's just Namco-Bandai, more characters is a higher possibility, but new modes is less likely since they tend to cut modes instead of characters these days. They already know Smash runs on characters more than anything else, so a bigger roster or at least some popular cuts back(namely the most popular or least redundant, so as much as Pichu tends to be popular in general, he wasn't as much in Smash, he's not too likely to come back. Young Link wouldn't unless he had something to separate himself from Toon Link. They do have different bodies, which could be enough for a semi-clone, though. But that's still work to do for Namco-Bandai, and with only about 2 years, as the dev kit for the NX came out on October 15, 2015, they need to be quite careful in their character selection).
In addition, there's licensing fees for other companies. Sega loves Nintendo, so that's easy to keep Sonic and Bayonetta. They have to go through two Capcom companies for both Ryu and MegaMan. It's possible one might not make it in, but I think they're likely to come back. Snake, well... Konami, nuff said. Then there's Cloud. He's hard to license in general, it's possible Sakurai was the reason he was in in the first place(whether cause he helped convince SE, or he's the only one who found him the best choice), so anything could happen. Namco-Bandai could have trouble licensing him for a 3rd game, and get someone easier(Lightning, Black Mage, maybe), or drop the SE stuff. Or we could get that DLC and more songs if lucky. Who knows. Should be a given which 3rd party is 100% guaranteed in the NX version if the rumor is true, though.
So I'm thinking it'll have a popular combination of both versions(stages, modes, etc.), possibly a different roster from the final one, and if the NX controller doesn't have a touch screen, a different Stage Builder, maybe one more similar to Brawl(but with more options like the Wii U version added on). This is of course assuming the NX is a console overall, and doesn't have some handheld variation.