Ben, any system I have used professionally has always had an external esata or similar type PCIE driven raid. Providing the Mercury Playback Engines what it needs to excell in performance (fast CPU/GPU/lots of ram amd fast raid system) is crucial to being happy with its performance.
With Avid you can get away with a lot less power since it is optimized to use DNxHD.
FYI, DNxHD plays nicely on my system. But I purchased it with the idea that it could handle whatever was thrown at it.
Sorry you are not having a good experience 🙁
Tom Daigon
PrP / After Effects Editor
http://www.hdshotsandcuts.com
https://www.youtube.com/watch?v=XRIg6h-LIm0
HP Z820 Dual 2687
64GB ram
Dulce DQg2 16TB raid