so like Im playing pokemon Y and I want to save and quit but it only gives me the option to save? do I just like go to the 3ds home window or is there an option for save and quit
I don't think there is a save and quit option like NL. Pokemon hasn't ever had a feature like that.
I just save (a couple times because paranoid) and then go to the home menu and close the game from there. You could also just press the power button after saving.