Ahem.
I'm sorry, what is Nier Automata?
I didn't even know who 2B was before I heard about her in Smash speculation. Sure, I'd seen gameplay of Nier Automata as it received lots of advertising, but to me it was just the game where weird gothic robo-stuff was happening and it looked cool but I was waiting for the next announcement. I knew about the blindfolded skirt girl, but I didn't know who 2B was until Smash speculation.
Now, show me how many people can say the same about FF7. That's right, a whopping .05%! FF7 is so legendary that people like myself who had never played the game until THIS YEAR know who all the characters are and can put names to faces. Before I touched the legendary game, I knew who Cloud, Sephiroth, Tifa, Barrett, Aeris/Aerith and Yuffie were; I knew about the use of materia and Mako and how it was destroying the planet; I knew about how Sephiroth's fall into madness; I knew about Cloud having emotional issues and his history of being manipulated; I knew Tifa was his love-interest and that she was a badass brawling *****; I knew Barret was also a badass and had a gun arm and an attitude to match; I knew Aeris/Aerith died and was killed by Sephiroth and that it was a massive moment in gaming history.
There are many more things I knew about FF7 and it's characters, and why is that? Because of how big that game is in the gaming sphere and basically now in general history. So forgive me if I feel like Tifa has more clout than 2B...but it's because she does! Also, calling her a side character is not only a disservice, but it's practically an insult. She's a titular character up there with Cloud and Sephiroth with her own set of memes and fan dedication and levels of iconic appeal, but I get what you mean.
In that case, yes, a technical side character from one of the most (if not THE most) well-known and iconic games of all time makes WAAAAY more sense then the protagonist from an existing IP that was brought back with pretty decent success. If you had to choose one or the other, the choice is clear that you would pick Tifa.
But as I said before, 2B is already in SC6 so her chances of being in Smash are already down due to that, and I feel like Tifa would be in Tekken if anything as she fits better there. To add to the Squeenix character chances breakdown here, Sephiroth would be better as an AT since being dedicated to him and keeping him balanced would be difficult. Lara Croft is essentially a shoot-mcgun character, really isn't as popular due to the new takes on her games and if you wanted to do a survival mechanic, as
EricTheGamerman
mentioned I believe...Resident Evil is the more iconic choice to fit that style. Crono, Neku, and pretty much any other Squeenix character doesn't have enough relevance or pull to be much of a contender. FF and DQ have their big bois already in the arena, so....
That really only leaves Sora and Geno. I can't see any other Square Enix characters making it in other than them.