Greninja doesn't struggle to kill at all. We have tons of kill setups coming from a variety of different moves and we can you into a lot of 50/50 situations. D-Throw -> F-Air is only avoidable by airdodging but if we delay the F-Air we can hit you regardless for instance.
Also footstool setups shouldn't be dismissed, Greninja mains are making use of them in real matches. Just look at Some:
You can't even pull the For Glory card here because one of these is clearly happens in a tournament due to the presence of a third player.
Greninja is a mix-up character and you can never be too sure of what he's going to do because he has many options to force 50/50 situations if he's versatile enough and good at baiting.