So word is going around that Sakurai and the team is having difficulties with the 3DS version. Specifically with multiple character fighters, which I can only assume are guys like Ice Climbers and Pokemon Trainer. Also in an article from Kotaku, Sakurai mentions that all the characters from Melee and Brawl may not make it into Smash 4.
Since they specifically mention the 3DS version, this may have something to do with the lag of transforming characters in multiplayer matches.
As far as potential cuts he talked about how difficult it was for 3rd parties to get involved with as well. I expect no Snake, as well as the majority of the Melee cuts like Pichu and Dr Mario. Brawl was a very good cast of worthy characters. And no, Lucario did not replace Mewtwo, the only similar animations they have are of Neautral B and Up B. if anything, the last minute Sonic addition booted Mewtwo who had more character data than any of the other 6 cuts.
I'd expect some of the clone characters to get cut if the Melee cuts are anything to go by. Mewtwo was the only character with a unique moveset from Melee to get booted. The clone characters could get relegated to alternate outfits. Sakurai mentioned in a recent interview that he felt custom costumes took away from the individual characters, but in context, it sounds like he was referring to just putting sunglasses or different articles of clothing on characters as opposed to different outfits each of these characters have worn. Who knows? The world needs more Robot Ness.
Sadly, it seems there's a chance Snake may be out though I find it encouraging that Sony used Raiden in Playstation All-Stars Battle Royale instead of Snake. No one would pick Raiden as a first choice. I figured Nintendo had a hand in that, probably in their original deal with Konami to include Snake in Brawl. Regardless of whether Snake ever reappears in another Smash Bros., perhaps Nintendo wanted to make sure he didn't show up any other fighting game that wouldn't be on Nintendo hardware. Or maybe Kojima blocked it because he wants to keep the door open for Snake to return to Smash Bros. It was bizarre enough that Snake made it in Brawl since the last time he appeared on Nintendo hardware was Twin Snakes, four whole years before Brawl. If Snake showed up in a Sony exclusive Smash Bros.-type game, it'd be even harder to justify including him in the next Smash Bros.
Fortunately, I'm confident that Sonic will return because Nintendo and Sega have a good working relationship and Sonic has seen most of his post-Dreamcast appearances on Nintendo hardware, including the next like five being Nintendo exclusive. Really, I want all characters with a unique moveset to be made a priority to return.