There are a few hard counters to classes like Bastion, but mostly soft counters in general.
There are even a few classes with no counters at all (eg McCree).
And yes, I think his stun combo is still pretty silly(they nerfed it several times already in beta) and I question the wisdom of having an aoe stun mechanic in a fps.
The big problem is that if he's paired with a Reinhart on say a payload map, you can't range them b/c of the shield, but then you definitely don't want to close the distance on them either (he shreds Tracer/Reaper flanks). So you end up having to rely on burst combos to stop payloads (widowmaker plays etc) and double winston setups etc