It wasn't considered truly overpowered, but a large part to why it is banned comes from its enormous coverage that makes it extremely centralising in the metagame. Depending on its set, Greninja can effectively deal with almost any Pokemon outside of Porygon2 or priority , which forces teams to pack more than one counter/check for Greninja. If you predict the wrong moveset, you are bound to lose one or two Pokemon.
Azumarill and other Fairies used to put a complete stop to it, but now with 40 Atk EVs and Gunk Shot they are toast. Even Chansey gets 2HKOed by 252 Atk Low Kick 93.8% of the time after Stealth Rock. The fact is that all its moves are viable options. One can just slap a Greninja on his team, give it 4 moves that patch up his/her teams weakness and it will work.
Greninja pretty much renders offense much harder to play with that crazy speed stat. People found its presence unhealthy in the meta and thus a suspect test was held. In my opinion, blocking teambuilding is one of the biggest reasons to ban a Pokemon. The fact that people had to bring up weird Pokemon like Tentacruel or Empoleon to try walling it is absurd.
Moreover, due to how centralising it is, the entire metagame revolved around it and if you try to adapt to it, it will adapt to you in return -Quoted from Smogon
Lets go through the Pro-Ban arguments and Anti-Ban arguments of Greninja.
-Large movepool, giving it near perfect coverage
-Protean granting STAB on every move
-Able to go mixed
-Little to no safe switch ins
-Has a very good matchup against Balanced and Offense
-Heavy pressure on teambuilding
-Unpredictability (If you predict X move and Gren has Y move, you lose a Pokemon.)
-4 moveslot syndrome
-Worn down by Life Orb recoil
-can be revenged with Scarfers and Priority
No doubt that Greninja is probably one of the weakest suspects to date in XY to ORAS, but whether you feel that it deserved to go is your opinion.