looks awesome. I wonder if he is a physical or special attacker.

double post.

Probably Special.

He has higher Special Attack

Rough base stat guessimates being 110 SpA, and 95 Attack, 120 speed

lovely. I guess I'll choose him. the story mode is better played with strong and fast pokemon. slower ones like chesnaut are generally competitive only.

Depends on your play style.  Early on a bulky poke is kinda meh, mid-late game they start to shine. Its good to have a mix. 

greninja used kage bushin no juts, oops, wrong game.

Funny thing is, subsitute will probably be used in a least 1 competative set to buffer his weak defenses.

What I wanted would be a mega to donphan and dragonite... (lucario and Ampharos are already confirmed, so half way there)

probably. and altough forbiden by smogon, double team's name in japanese is kage bushin so we get a full ninja.