Here's a way we could bring back cut characters in this game:
Let's say that we end up with four unfortunate cuts this game; Snake, Ivysaur, Squirtle, and Wolf (although if you wanted, you could swap this with Ike or Jigglypuff). Obviously, due to third-party issues, Snake won't be able to return in any fashion, but what about the other three? Well, these cuts are
initially for the 3DS version and are not permanent cuts. Ivysaur and Squirtle were almost certainly cut due to technical issues surrounding their inclusion and Wolf was almost certainly cut due to not having enough time to finish him. Considering that Sakurai has went on the record to say that he recognizes that
every character has its own fan base and will do his best to bring them back, he may have to find alternate routes to including these characters.
So what can he do? Use the time between the 3DS & Wii U release to finish ironing out issues with Squirtle & Ivysaur and to finish up Wolf. That means that they'll be able to include all three of these characters from the start on the Wii U version. At the same time, release all these of these character in a pack together as free DLC on the 3DS version for everyone to download. This would mean that the concept of universal roster Sakurai has spoke about would still remain true, the roster would be better overall, and we only have Snake as a permanent cut. Characters like Roy, Dixie Kong, and Bowser Jr. could also make it into the game in a similar fashion; only real difference would be that they weren't Brawl veterans.
Then here's another idea I could see happening specifically for a 3rd gen rep (Blaziken, Sceptile, maybe Plusle & Minun):
The roster for SSB 3DS & Wii U is already finalized. Assuming that planning for OmegaRuby and AlphaSapphire started a year before Pokémon X & Y is released; that would mean that the roster had already been decided and as such, a 3rd gen character cannot get in. However (hypothetically speaking), the Pokémon Company is made aware that Sakurai is doing character DLC in this game. Knowing that a 3rd gen character can't be in the initial roster yet still wanting one in Smash, the Pokémon Company seizes an opportunity to push for a 3rd gen rep. Eventually, Sakurai caves in and begins work on adding 3rd gen character/stage as DLC (let's say they start work on July, 2014).
Then on mid-September, 2014, Sakurai announces a new DLC package for the 3DS version, but does not specify. Despite speculation over cut veterans being added back together or even a very highly requested newcomer that missed out on the initial roster, it is revealed at an early October Nintendo Direct that it is a DLC package packed with 3rd gen content. Blaziken is revealed as a playable character, Sootopolis City is revealed as the 3rd gen stage, and musics from OmegaRuby and AlphaSapphire are also present (costing $5 to get initially, although when promotional values runs out, is later made free). It is then highly promoted until the DLC releases in early November, 2014; in time to promote the release of OmegaRuby & AlphaSapphire later in the month. Not only that, Blaziken, Sootopolis City and music from OmegaRuby & AlphaSapphire are also made available from the start on the Wii U version as they have also been working on putting them on the Wii U version.
I don't think either scenarios are too far-fetched here. These are things, while not guarantee, are things I could see happening with DLC. Everyone (well, almost everyone) wins and they make sense from both a business perspective and Sakurai's perspective.