I think Waititi's issue for most people is that he's probably less consistent than Gunn.
I agree that the best of Waititi's stuff, like What We Do in the Shadows and Hunt for the Wilderpeople, is probably better than anything Gunn has done, but he also is capable of crashing the car into a tree in a way that Gunn hasn't so far.
For example, I love Peacemaker and Our Flag Means Death, but there's no question that Peacemaker is a much better show, top to bottom, whereas there are a lot of times that individual Our Flag Means Death episodes could have used another pass or two.