So, I leveled up Mewtwo all the way to 100, and learned that signature move he gets at this level, and got the footprint badge.
After that, I tried going through Elite Four again. Defeated them with only using Mewtwo, X mega evolution with Recovery, Psystrike, Psycho Cut, and Aura Sphere, with plenty of items. Despite the ineffectiveness on some of their pokemon, I'd say this was pretty okay. Also, I got mroe than 3,000,000 to spend on shops or whatever items in the game.
I wonder if I should try pokemon Y starting from beginning again for the case of new pokemon, and just transfer Y pokemon to X or something. Though I have both X and Y downloaded from eShop, I got a cartridge boxed pokemon X for christmas.
I've got a 3DS XL from before, and just got a 2DS this christmas. I wonder if I should see what happens if I register both of them as separate FC's and see what pops up in friend safari.
Also, Pokemon Bank apparently confirmed to not have solutions against hacked pokemon.