I think so
At 131/131/99 Offensive Stats and a Physical Movepool filled with all the tools he needs, I'd say that a Bulky Attacker Set is worth it since his Attack is just as poweful as his Special Attack
And although he has a more Specially inclined Movepool, his access to STAB Sucker Punch and Acrobatics, Shadow Claw, and Roost, he pull such a Set off well.
"Is there a way to Reset EVs?"
Yes, through one of the Core Training Bags called a Reset Bag. You can earn one through participating in Super Training Exercises, or more likely through your Pokemon finding one during Core Training. That's how I found mine.
So, yes, I would keeo that Yveltal, a Physical one isn't exactly bad, it's just different- I'n fact, I'd say unique. Just Super and Core Train other Pokemon until you come accross a Reset Bag, and I would Train him in HP and Attack.