Okay, so after a partial set against @Storm179 (partial because I was too salty to continue), I was shown just how much S3 has changed this matchup towards HIsako’s favor.
@developers I can understand why you might make changes to make a certain unfair matchup fair, but why on earth would you take a relatively fair matchup and crumple it up, light it on fire, throw it into a vat of acid, and roll it down the hill-side into an exploding volcano? 
@Infilament I’d like your input on this matchup, since you’re so good at analyzing things. Also, I’d like you to point out any mistakes/assumptions I made below and correct them. 
@Storm179 I’d like your input, since you’re officially, as of now, the best Hisako player I’ve ever seen (and I genuinely mean that). I think you could offer a unique perspective since you’re on the other side of the fence during this matchup. 
First, her long-reaching grounded heavies - her d+HK in particular. Thanks to S3 changes, it now bypasses Aganos’ chunk armor. In S2, this wasn’t so much of a problem, because it could easily be absorbed and punished accordingly. However, now that it’s a legitimate threat, it gives her a brand new mixup she didn’t have before. Even worse, it comes out so fast (for a heavy attack), you can’t even jump over it, because it’ll catch you in the pre-jump frames - although according to Storm, this was true in S2 as well (but I never knew that because I never had to try it thanks to the chunk-armor). This gives her a free and devestating mixup. She can:
a) use d+HK for a hard knockdown, giving her options.
b) use a command grab for straight damage or full-combo punish (depending on which 1 she does).
c) use a jumping attack, like her in-air on-ryo-zan for an overhead.
In regards to the low attack, I find that the only thing I can do is shadow ruin it or block. If I block it, she can do it again before I can let go of the block and counter-attack. Shadow ruin, while good requires meter, which is something you generally want to save against Hisako to avoid the command grabs or to catch her out of the air.
Hisako’s command grabs can be devestating, and thanks to Aganos’ rather large hitbox, he’s probably the easiest person in the cast to grab. While it’s nice to see that shadow pulverize now works on possession in addition to influence, it’s still a disadvantage for Aganos, because he has to save it as a precious resource to counter it rather than being able to use it on other things, and even that’s not guaranteed, because she can hit you with the command grab as a linker as long as she has wrath meter and continue her combo to deadly effect. Sure, you could jump it when it’s done outside of a combo, but you have to know that it’s coming and that isn’t always so easy. Not only that, but attempting a jump opens you up for the aforementioned mixups listed above.
If you block her d+HK on wakeup, it can open Aganos up to another mixup by way of possession, which again creates a hard knockdown, giving her advantage.
Her in-air on-ryo-zan is probably the weakest choice for a mixup on wakeup, but it’s still a useful tool for her if you’re trying to jump to avoid her command grabs. Even worse, it recaptures with shadow or wrath, making it even scarier than you might think.
Her teleport, in S2, was easy to deal with. I could chunk up while she did it and absorb whatever she had coming, jump her command grabs, or simply jump backwards for a crossup (my personal favorite). You’d think that the speed-gain on Aganos’ chunk-up in S3 would help out, but sadly, that’s not the case. S3 also introduced a speed-boost to her teleport. In fact, if anything the matchup with Storm has shown me that chunking up when she teleports in S3 is an instant punish. In fact, she can hit you (again with the d+HK) before you even get the chunk in, so you can’t even gain the benefit, despite being hit. Even worse, she now has the ability to cancel a teleport into ANOTHER teleport - this gives her ANOTHER mixup and makes for some crazy mind-games, all of which are in HER favor.
Another option she can use to her advantage that I forgot to mention is her d+HP. This little diddy can be useful for hitting a jumping Aganos or even 1 that’s trying to cross-up. This move is so good, I’ve seen Aganos fully on the other side of Hisako and still get hit by it, even though the tip of the blade is nowhere near him (must be that ghostly magic). This is yet ANOTHER example of a potential mixup that Hisako has against Aganos AND it’s a grounded heavy to boot, which means, sorry chunk-armor - you need not apply, even on the ground. Worse yet is the fact that it launches Aganos high into the air, giving her juggle, recapture, and flip-out options, which means more mixups - YAY!!! 
…and I haven’t even gotten to her counter yet. Then again, I probably don’t need to, because from Aganos’ perspective at least, not much has actually changed there.
Her whole gameplan, it seems, is to knock you down. In S2, this wasn’t always a problem because of the chunk armor, but in S3, because she can ignore the chunk armor, it practically makes her the defacto winner in this matchup. Even worse, if you’re lucky enough to have walls up, this makes it even easier for her to bring them down, even moreso than it already was in S2 with her double-bouncing ender.
So, fellow golemites - what can we possibly do against Hisako? From what I’ve seen, the answer is NOTHING. She is custom built to train the golem into doing what she wants and/or simply knocking him down. If that isn’t true, then please, by all means, enlighten me, because the tiny, pale girl makes me want to cry… 
And if the situation is neutral, descent mix-ups are pretty much never in Hisako’s favor - everything she can do out of it is wildly unsafe. I highly recommend punching Hisako in the face when she does this move in neutral. Out of all the options she has, counter is the one thing she’d really rather not have to take a chance on in most situations.
Your job as the opponent is to not give her what she wants, to make yourself as untrainable and unpredictable as possible. That aspect of the fight has not changed at all.
