So since I learnt how to punish Homing Spin properly on shield, Sonic has been so much easier to deal with.
I think the ability to punish HS on shield takes away a lot of (almost all, really) of Sonic's shield pressure from the air. It stops him from being able to do things like HS into you, whiff, and double jump before he hits the ground, or HS into your shield and just bounce away -> jump safely. He also can't seamlessly transition back into Spin Dash for free after a Homing Spin hits your shield.
Playing as other characters has also made me appreciate how good Greninja really is at dealing with Spin Dash on shield. A lot of characters simply don't jump high enough to actually hit Sonic after he Spin Dashes into their shield and jumps, so he gets away with it for free. Characters with high jumpsquat and short jumps struggle to actually get away from Sonic's mixup of simply stopping Spin Dash rather than jumping, which Greninja doesn't have to worry about because he jumps away safely no matter what.
Sonic is still a strong pick against us, but whether I'm convinced he actually beats us now is a different story. Some characters can punish Homing Spin on shield but not all (you need good air speed and preferably good range on your Fair, or a move called Bouncing Fish) which gives Greninja a fairly niche advantage, and not all characters can actually punish Sonic when he jumps after hitting your shield with Spin Dash. Greninja has a projectile which is safe to use from afar (shurikens still have relatively low ending lag for a projectile despite the nerf) and his frame 3 jab is fine for stopping Spin Dash if you want.
Also, Greninja might just be the best equipped character for punishing Spring > Dair because he has a lot of options against it. Hydro Pump can stall Sonic in the air, we all know how good Greninja's dashgrab is if you want to grab Sonic's landing, and Greninja's Usmash is not only powerful but the first hit of the sweetspot can't be clanked with. Plus if Sonic Dairs from the proper height to get no landing lag, he will have no hitbox on the Dair when he's near the ground, so Usmash should be a free hit.
Sonic is not easy to deal with by any stretch of the imagination by the way, he's an extremely annoying character who can turn the tide of a match quickly and easily camp you out if he gets the lead. But I have at least personally come on leaps and bounds in this MU. Looking at Greninja's tools in this MU makes me think he has a better time in it than most. It's early days, and I'd need to fight more good Sonic players to say for sure, but on a theory level I don't see why we couldn't go even with Sonic at this point.