When going against Atlas, hard cc (Silence, Cripple) shut him down, as he relies on his abilities rather than his primary

Saati's reveals counter Sha and she also has the range to fight him if she gets the first shot. Having Seek (Increase the duration of Dead Ringer’s reveal on destruction by {0.5|0.5}s) on high levels hard counters him, especially Sand Trap.

Vatu needs to come close to your teammates to deal signifant damage, so if you are playing cripple always keep an eye on them and cripple him as soon as he dives

You can negate the seedlings damage by using obliteration, especially when fighting close to her as it will also damage her.