The thing about Ness is that you really can't safely get near his shield because of OoS Nair. His Nair has more range than it looks, so if you try approaching with standard Greninja stuff, you're going to get punished. Not to mention, if you approach with a well-spaced Fair, there really is no way to safely punish an attempted OoS Nair. I found the best option is to simply outcamp him with Water Shuriken and stuffing his aerial approaches with a well-timed Usmash. If he predicts it and tries to airdodge, you get a free jab (not sure if this will be true in v 1.0.4, but I'd imagine it would be), which will still send him away. Btw, and this applies to jabs and any grounded multi-hits, if you get trapped in PK Fire, DI toward the ground as much as possible. Greninja has a very weird quality where his landing box is lower than most characters (this is why he absolutely cannot land on BF's top platform from a single jump at the bottom level despite appearing to be above the platform when he jumps. Even Uair won't get him on top of it. The game thinks Greninja is still technically below the platform because of his weird landing box. Only Dair, which makes you jump a little higher during the animation will allow you to get up there without a double jump). However, this is extremely useful as it allows Greninja to very easily escape quite a few ground multi-hits, including PK Fire.
Another thing regarding Ness is that he is a floaty character, so Hydro Pump generally won't be able to really gimp him in any sustainable way if he's already fairly high up. You need to get him to use his double jump and hit him afterward. If you manage to get him level with the stage or just slightly above it offstage lacking a double jump, he will be forced to use his PK Thunder, but be wary of when he can and cannot make it simply by holding the control stick toward the stage. Once you know he's forced to PK Thunder, don't jump off-stage until you see him starting the move up. Once he does, Hydro Pump immediately in a way that the stream hits him as fast as possible. You don't need to be fancy; you just need even the smallest push to mess his recovery up, but you need to do it quick and accurately. Once he uses it, you have almost no leniency; you need to act as quickly as possible. Some other useful things to note are that Dair cancels PK Thunder out like most projectiles, and to be extremely careful when above him. PK Thunder has been buffed in this game, so you want to try and get away from him as quickly as possible so that you can fall to the ground before the move reaches you and so that you have ample time to react if he tries to hit you with PKT2 instead.
Finally, be very wary of grabs. Ness can combo out of them at low percents and kill with Bthrow at higher percents. Luckily, our jab is fast enough to usually get through any shield grab attempts, and if we find him shielding our multi-hit jab, wait until the his shield is just out of range for the multi-hit to end it with the final hit (which has more range than jab 3 actually, believe it or not). If he tries to punish it with a running grab, we can roll away, spotdodge, or jump; if he drops his shield early, the final hit of multi-jab will create more distance between you two, and if he rolls toward you, we can roll away, jump or spotdodge before he can turn around and grab. If he shields your first jab, you can still get out before he grabs you, but be careful of him predicting a roll or the spotdodge. On the odd chance that you throw out a jab three at max-range and he shields it, I'm pretty sure he still can't punish you if he shields it unless he predicts your next action (bar jumping, but that puts you in a slightly disadvantageous position in this MU).
I think Ness is overall a fairly tough MU for Greninja since Greninja has to play it slightly unconventionally and *gasp* our approaching options are greatly limited due to OoS Nair being such a good move, but I still feel it's in our favor. As long as we avoid Ness's grabs and PKT2, he has a fairly tough time killing us since Usmash outranges all of his aerials iIrc. You just need to play the MU fairly safe and keep Ness the hell out.
This is pretty much what I've learned from playing a local Ness who's been playing the character since Brawl, so if I missed anything or if I made an error, please inform me.
