Little Mac may be the kind of guy that you can really root for in a fight,but it’s just not enough to stop Greninja. Greninja is much faster in combat and while he may lack Little Mac’s sophisticated punching techniques…he would win in a close combat fight. His attacks deal more damage than Mac’s and Greninja has enough defense to endure any of Little Mac’s punches. Greninja wins.
DReager1.com 
Plus if it gets into long-range Greninja can whip out his Water Shuriken before Mac gets close
Greninja definitely has a massive advantage at long range. There would be no way for Little Mac to get any shots in. Greninja could throw those shurikens all day until they defeated Little Mac, but I have a feeling that one would be enough.