Having played against a greninja for 1 hour, the least I can say, is that Ike's pretty weak versus Greninja in every way.. Except maybe his aerials and jab.
Given that Greninja has excellent ground and air speeds Ike can't really play his cards right, since he mainly relies on his neutrals, a bit too slow versus Greninja, and the area covered by them. And Greninja just dodges, jumps, dash grabs and eventually finds his way, playing with Ike's lags.
Moreover, Ike's recovery is destroyed by Greninja's Up-B. And I won't remind you how awfull Ike's recovery is. It doesn't take that much to be lost beyond recall after a recovery attempt, if you know what I mean..
The only pro I've found so far is that Nair and jab tend to nicely control the space, but once again, Greninja's speed will punish you if you didn't manage to hit.
I'd put Greninja in the "characters I feel bad to play against" basket, alongside Marth and Sheik since the effort you have to make to defeat them is half what they do to defeat you.
So go ahead and teach me guys, cause I'm not blaming Ike and I'm not good enough to state that Ike's bad against such or such character, but as a result I'd say that Ike's MU versus greninja would be 30:70.
Yet, let's keep fighting for our friends.