I fly wkm and pixhawks, and just naza-m from Phantom, so no expert on Naza. But in general:
Naza: Easy and fast to set-up.
APM/Pixhawk: Complex, powerful, and extremely customizable, significant learning curve.
If you just want as close as possible to RTF, want to simply fly around, or do photography/filming with easy to integrate sub-systems (iosd, zenmuse gimbal, lightbridge), and want to get going fast go Naza.
If you want to fly fully automated missions, be able to analyze flight characteristics, look at flight logs, use a system that can be expandable or upgradable(e.g. better gps, sonar), choose from a wide array of different flight modes, go Pixhawk.
As of Ardupilot 3.1/3.2 I find them both comparable in terms of performance/stability (Naza atti and GPS vs Pixhawk Alt Hold and Position Hold). Ardupilot has an edge imho when it comes to reliability, as it is opensource and problems can and are better identified, analyzed, and remedied by a large community. DJI is silent on any issues, won't admit to them, and support is inexistant.