When the opponent does War Destroyer, if you are in the air, immediately knee dive to get out of the air. (this is assuming you are not directly over him) From here, if you have time, you can do one of two things. Wave dash out of the way from the decending missles, or you can counter super. Wave dashing out of the way is your best bet, then you can punish them without having to take any damage.
With chun, you shouldnt knee dive into the bubble immediately. Gold War Machines smart bombs, and shoulder cannon keep him in the air, use them. When she does the super, smart bomb>shoulder cannon>smart bomb>shoulder cannon> untill it runs out, then punish her because she has insane recovery time.
With ryu, rush him down. He should only hit you with the shin shou “maybe” once for free. And that is the start of the round when he has one level. After than, get on his ass. He wont be able to build level and he is not agile enough to play run away with you effectively. His normals arent fast enough for him to poke you safely. Basically, you chip the hell out of him untill you have 3 levels, dual and kill him.
Also realise that none of these people can do these things for free unless they have maximum range. The easiest way to nullify your problems is to learn to stay up on them. It will make them alot more cautious about doing supers. The first few times they do a super at point blank range and then get rh>war destroyer from you as soon as they finish they will regret it.