They're both awesome!Ninjask is fast as F-k Boi,and Shedinja is a invincible ghost(just kidding).I would choose both of them!But if you wanna have only one,well i'll give you the (possible) best movesets and stats for both of them in my opinion:
Ninjask
@Focus Sash/Leftovers
Nature:Adamant(for a bigger attack)
Ability:Speed Boost
Moveset:Double Team(It will be harder to hit Ninjask if you use it a lot of times)/Protect
Swords Dance(Raises Atk,and we know that Ninjask is an Physical Attacker)/Baton Pass(how others say)
Fury Cutter(Power doubles if it hits + STAB)
Slash(Pow.70 Acc.100)
Other moves:Aerial Ace(Pow.60 Acc.∞ + STAB)
Leech Life(Pow.80 Acc.100 + Recovers Hp + STAB)
Shedinja
@Focus Sash
Nature:Adamant(Raises Atk,so the Physical moves that I recomend will have a bigger power)
Ability:Wonder Guard(It's the only ability that Shedinja can have,so,yeah)
Moveset:Leech Life
Dig(with Wonder Guard,Shedinja cannot be hitted by Earthquake)
Aerial Ace/Metal Claw(for Rock types)
Confuse Ray/Shadow Ball
Other moves:Giga Drain(for Water types + Recovers Hp)
Double Team(to dodge Dark,Fire,Ghost,Rock attacks.)