As a name of topic says: how to counter this infinite jump ins, jump outs and neutral jumps with Aganos? Especially neutral jumps after Aganos were hit by hard knockdown. What is best tool for it?
Shadow Roll works well I think if it isn’t a meaty. If it is a meaty,block.
Just get used to waking up with down+back (even if they throw you a few times), and use up flick (back+LP I believe?) when they jump. It’s a very fast anti-air.
If anyone jump towards me when Im Aganos…I make sure Im always chunked up and I crouch HP right through their jump and knock them down, then re-chunk. REPEAT.
If you jump at me your getting hit
Always bait the jump when your chunked. If they get in grab through them. Play the chunk game and you will go far.
If you are on wake up, block and and then asses the situation from there. Stay chunked up.
It’s not working if opponent making meaty.
If it’s a meaty jump-in, then you block or shadow ruin (so long as it’s not a a safe jump).
Shadow ruin wiffs
Then your only option is to block. If they are following up with buttons consistently then it may be possible to shadow counter, but otherwise, you’re just going to have to block it out and try to avoid getting thrown in the meantime. Aganos doesn’t have great defense once the opponent gets on top of him and tosses out a legit setup.
Aganos vs rushdown eyedol OH GOD 
It depends on whether or not you have armor. If you do, you don’t even have to worry about anti-airing characters that don’t have multi-hitting jump attacks (which is most of them). Just release block, take the jump attack, then hit them during their landing frames with something like cr.MK into Natural Disaster. If they’re smart, they’ll start doing empty jump into throw. You can then be smarter by beating it with a neutral jump HP on reaction.
On wakeup, you can really only do something about it with meter. But really, jumping is the easiest thing to deal with on wakeup because it’s way more reactable than a heavy meaty/throw mixup. Shadow Natural Disaster deals with any jump that doesn’t hit very low, including crossups.
What about if I got no chunks?