Greninja/Pika is probably even. Pika gets insane close range pressure, really nice low percent combos and some kill combos that work well on Greninja's fall speed class. Greninja has a very unique anti-QA tool in Hydro Pump (can be thrown out in neutral, beats QA cleanly and allows for probably the hardest feasible punishes in the game) and is one of the only characters who can feasibly gimp Pikachu. Plus generally higher mobility and range. Greninja couldn't punish Pika on shield anyway and Pika now doesn't get free dashgrabs from a shielded Fair so funnily enough, Greninja probably benefits more from the patch in this particular MU.
Greninja/ZSS we SHOULD lose but don't in practice. It's incredibly weird. She just doesn't overpower him in neutral like she should, and if she can't get her kill combos she will struggle to kill such a mobile character with Bair spam or Up B OoS. Prepatch we couldn't touch her shield with a barge pole, now we have multiple moves with which to pressure her. Greninja is generally better at killing her (Usmash can kill any flip jump overextension with good reactions) but doesn't punish nearly as hard. Greninja did quite like his shield in this MU, with the new patch this might move to her favour because she just got SO dumb, although he couldn't punish Nair. Again I don't see much changing but I think this hovers between even and 55:45 Zero Suit.
Shaya
what exactly happened to paralyser? Why is it worse on shield? Do you know if shurikens are better or worse on shield?
Greninja/Ryu no idea. Keeping him out and running away from him isn't hard in my experience but I haven't played a really good one.
Fox I feel got better with the patch. Again, Fox always destroyed our shield, but now we can actually poke at him and try to wall him out with Fair and Ftilt without constantly getting hit by OoS dash attack. As we get better at resetting to the ledge with Hydro Pump to stop his dash attack landing punishes, and also edgeguarding him, I can see this approaching even.
Sheik still beats us but I don't think she destroys us as bad as before for similar reasons to Fox.
I don't think Sonic beats us and haven't done for a long time. It really is as simple as learning how to deal with Spin Dash and reacting to his dash ins. He doesn't exert the up close pressure you usually need to beat Greninja, despite his mobility.
I do think we lose to Wario and Toon Link. The former just outbuttons us and has annoyingly good mobility, the latter creates the hardest zoning wall in the game for Greninja to get through. We may also lose to Diddy, he can lame us out and neutral and though matches with him are always close, he usually pips Greninja to the post. This happens a lot at high level if you watch Some and other Greninjas. I don't think we exploit his recovery enough though.
Our best MU is Ganondorf most likely, Jiggs isn't that easy to beat.