Nah, Thor is like a million times stronger, more durable, and more experienced than Cap plus he's can control the weather and you can't possibly think Cap can defeat a tornado (he's also faster and more agile).
Cap was way overpowered in the EMH episode, I can understand him outmaneuvering Thor a couple of times but they went too far because Thor is clearly a warrior with over a thousand years worth of combat experience. Thor was portrayed as too much of an oaf in EMH in my opinion, it's like they forgot that he's actually a skilled warrior.
Exactly
I don't see how anyone would think that Cap should ever "wipe the floor" or even stalemate Thor besides I'm pretty sure Thor was trying to subdue him in EMH without harming him.