Greninja fully deserved his ban. There are no Pokemon that can counter him reliably. There are CHECKS, but not counters. Every time you see a Greninja, you are forced to either sack a Pokemon to go into your scarfer or whatever or get a lucky switch. Even then he can just switch out. Getting low kick made it so that Chansey can't even wall him reliably. Also please don't try to think of obscure walls because even if one or two did exist, that's not enough, and even then, they would have to be played on every team just to counter Greninja, so finding one or two obscure walls is not the objective here.

The main difference between Smogon and VGC is that Smogon is a singles format and VGC is a doubles format. This is why certain Pokemon are OK in VGC and not in Smogon. It's because Gamefreak balanced the game around a Doubles format, which makes some Pokemon inherent problems in singles, that need to be banned, while being totally fine in Doubles. A perfect example of this is Mega Gengar. A Doubles format has easy ways to deal with him. Singles doesn't. Same for Smogonfrog. Doubles has ways to deal with him because having counters isn't as important in a Doubles format. Not in Singles.

R.I.P in Ubers, Edgefroge.