Laijin
Smash Hero
Young Link does better against Puff than most of the mid and low tiers(except probably Doc), but not as good vs Fox, Falco,Falcon and Sheik.Young Link is significantly better vs Puff than Mewtwo is
Since Puff is not only the best character but also belongs in a tier of her own
This makes Young Link better
Has an alright MU vs Peach, Ice Climbers and Ganon.
I don't think Mewtwo has good match ups vs any of the high tier characters. Except probably an alright MU against Falcon and Ganon.
tl;dr Young Link has better MUs overall than Mewtwo