What version of Arducopter are you running?
I'm running AC 3.3-rc 11, yeah the new AC is pretty good, been only seeing the positives and not the negatives others have been having but in their case it's almost always down to config/pilot error.
I actually started with the APM on it pre Pixhawk days. Did a lot of testing but needed to move on so eventually put a Wookong on it so I could get to work. But I still have a Pixhawk on my hexa which I've set up for mapping and it's working fantastic!
Every tool has it's purpose and I agree, the DJI stuff may be better for AP/AV but it's almost as if AC was made for mapping. I love it. They're like Mac and Linux, both have their purpose
It's just amazing to watch it go through it's automated missions and come home to a perfect landing.
I'm in awe every time that thing lands on auto, blows me away at how smooth the landings are.
I think the combination of the new Pixhawk 2 with it's internal stabilization and the new firmware will be a real winner.
We're all pretty hopeful, just with it would get here already hehe