Atlas Shield shuts down Skye's Ult completely, so try to read her mind and time it correctly when u believe she has her Ult ready.

Atlas Deja Vu is great counter to seris group burst heals as he can setback enemies to their lowest hp

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

try to predict where he'll land, if you can cripple him he's a free kill with your combo