Before I go wrecking my quad, I'd like to confirm that I picked up everything from this video correctly. Here's my understanding of how to tune a quad:
Disable all the fancy stuff so you only have raw PIDs messing with your flying. Only enable them if you still have problems after tuning. Start with P values to get your preferred sensitivities in. Next, fiddle with D until you get a good balance between control responsiveness and bounceback control. After you get P and D set, play around with I to make you feel either floaty or on rails. When all that's set, test for the problems that those fancy filters are meant to fix (i.e., for anti-gravity throttle punch to see if a corner dips or not) and turn them on as necessary.