My guess is because they don't want to create a divide where some people will be advantageous with the motion controls (faster aiming) and others using traditional controls will be at a disadvantage.
And it seems that the general perception of motion controls is negative, so a lot of players will have it disabled, then they will get owned online, then that might negatively impact the game's sales performance or something like that. Given how popular the FPS genre is, shaking up something fundamental such as the control scheme is very risky. You can't simply have it as an option, because you'll instantly put a lot of people at a disadvantage - a risk a lot of developers don't want to take.
I love Splatoon's controls. I personally hope it catches on.