が is a subject marker and を is an object marker.
In the first sentence the subject is 何が. And the object of します is not specified.
On the other hand, in the second sentence the subject is not specified. It may or may not be
you, depending on the context. Instead the object of します is clearly indicated by the object marker を.
So, the first sentence literally translates as something like
What will do? or it may mean "What is the agent that will do?" It doesn't really make sense as we don't know what the agent is supposed to do. This is absolutely different from
What will you do?