You would have more control over what you are doing in Agisoft Photoscan, meaning that you would be able integrate various python scripts to increase efficiency and automation of processing in Agisoft Photoscan. Pix4D on the other would be limited in the terms automation. You would still be able write some basic scripts in a Command Prompt or to a .bat file since Pix4D doesn't support python internally.
They are both capable of Aligning Images, Generating a Point Cloud, Generating a Mesh, Creating a DEM and Creating an Orthomosaic.
I have processed about 4000 projects in Pix4D and about 300-400 projects in Agisoft Photoscan. Based on my experience Pix4D is easy to use and understand and it is reliable but it has limited capabilities in terms of controlling the processing parameters. As for the Agisoft Photoscan on the other hand it is more difficult to understand and use compare to Pix4D however you would have more control over what you are processing. And for the outputs I found Pix4D to be much more reliable for Multispectral and Thermal projects as for the RGB's and DSM's if you use the highest settings in Agisoft Photoscan you are most likely gonna get more detailed outputs compare to Pix4D. They are both really powerful softwares, it comes down to personal preference.