What practice for designing a 3/4 top down game?

I'm working on a top-down 3/4 perspective game similar to A link to the past, I've built the game both in 3d with an orthographic camera at a 45 degree angle and built it using 2d. So my question is which way is better for this kind of game style? What are the pro's and con's of each so I know which would work best down the line?

 

If the assets are in 3d don't use ortho. Instead pull the camera way back and zoom it in so that you can keep some of the perspective, but still have it play well.