I'm a WFT main and my roommate is a Marth main.
OOF. *clutches heart*
The key thing to remember with Wii Fit Trainer is that she will never, ever, ever win in neutral. So you need to stay on the move and be flinging projectiles around like crazy. The new Header physics are so much easier to hit with, and when the opponent is getting desperate to rush into you, that's when you smack them in the face with Sun Salutation. She's very good at frustrating the opponent.
Another point is that you should never use Wii Fit Trainer on Final Destination. She benefits SO MUCH from the Battlefield platforms, because they let you toy with Header (which now no longer gets stuck above the platforms like it used to). Those platforms also keep the opponent above WFT, which is the #1 place nobody EVER wants to be.
That's my anti-sword strategy. Stay on the move, spam projectiles, frustrate the opponent, platform shenanigans.