Ken, maybe you can list some of the methods you use to determine what needs to be changed in the basic Multiwii setup during the build. I got my Multiwii from ReadyToFlyQuads and it was pre-loaded with the approprite firmware for my Octo so there wasn't a lot to change but I know that if you obtain it from other suppliers that it could be close to a blank slate. The info may be helpful to those considering the Multiwii but may be a bit gun shy because it isn't a plug-n-play FC.
I have to say the first thing I noticed on my FrSky Taranis was the number of switches and pots that are available. Fortunately I only had to wait 2 weeks for it to be back in stock at a US based company. 1 hour after I ordered it, it was again out of stock. It definately is a hot item.
I ordered my Taranis right after the first batch hit the USA and wait times were measured in months, now I hear it's down to a couple weeks usually but you do have to grab one as soon as they hit stock or wait again.
I don't recall where I found this or who the author was, but it has proved to be a very good guide to tuning not just the Multiwii but any controller that uses a PID based firmware. If you look at the section General Guidelines, that is pretty much how I tune mine. I use the M/W on small quads almost exclusively so I start with the default settings and go from there, they seem to be pretty close for a standard 350 to 550mm quad. Only ones I use very different settings on are my aerobatic quads that only ever get flown in manual mode, ever try a flip with autolevel accidently engaged? ...

I disabled it after the rebuild...
Here's the tuning guide, author unknown...
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PID tuning theory and configuration guide for MultiWii
Now updated for multiwii >1.9
P is the dominant part of PID and gets you in the ballpark for good flight characteristics.
Basic PID Tuning - on the ground
Set PID to the designers default recommended settings
Hold the MulitiRotor securely and safely in the air
Increase throttle to the hover point where it starts to feel light
Try to lean the MultiRotor down onto each motor axis
You should feel a reaction against your pressure for each axis.
Change P until it is difficult to move against the reaction. Without stabilisation you will feel it allow you to move over a period of time. That is OK
Now try rocking the MultiRotor. Increase P until it starts to oscillate and then reduce a touch.
Rrepeat for Yaw Axis.
Your settings should now be suitable for flight tuning.
Advanced Tuning - understanding impact of P, I and D
P - proportional
P provides a proportional amount of corrective force based upon the angle of error from desired position. The larger the deviation, the larger the corrective force.
A higher P value will create a stronger force to return to desired position.
If the P value is too high, on the return to initial position, it will overshoot and then opposite force is needed to compensate. This creates an oscillating effect until stability is eventually reached or in severe cases, the overshoot becomes amplified and the multirotor becomes completely destabilised.
Increasing value for P:
It will become more solid/stable until P is too high where it starts to oscillate and loose control
You will notice a very strong resistive force to any attempts to move the MultiRotor
Decreasing value for P:
It will start to drift in control until P is too low when it becomes very unstable.
Will be less resistive to any attempts to change orientation
Aerobatic flight: Requires a slightly higher P
Gentle smooth flight: requires a slightly lower lower P
Integral
I provides a variable amount of corrective force based upon the angle of error from desired position. The larger the deviation and / or the longer the deviation exists, the larger the corrective force. It is limited to prevent becoming excessively high.
A higher I will increase the heading hold capability
Increasing value for I:
Increase the ability to hold overall position, reduce drift due to unbalanced frames etc
Decreasing value for I:
Will improve reaction to changes, but increase drift and reduce ability to hold position
Aerobatic flight:
Gentle smooth flight:
AP: Requires a slightly lower I to minimise wobbles / jitter
D - this moderates the speed at which the MultiRotor is returned to its original position.
A lower D will mean the MultiRotor will snap back to its initial position very quickly
Increasing value for D:
Dampens changes. Slower to react to fast changes
Decreasing value for D:
Less dampening to changes. Reacts faster to changes
Aerobatic flight: Lower D
Gentle smooth flight: Increase D
Advanced Tuning - practical implementation
For Aerobatic flying:
Increase value for P until oscillations start, then back of slightly
Change value for I until until wobble is unacceptable, then decrease slightly
Decrease value for D until recovery from dramatic control changes results in unacceptable recovery oscillations, then increase D slightly
Repeat above steps
For stable flying (RC):
Increase value for P until oscillations start, then back of quite a bit
Decrease value for I until it feels too loose /unstable then increase slightly
Increase value for D
General guidelines:
For stable flying with less wobble / jitter ( AP / FPV):
Lower P if you have fast wobbles
Lower I if you have slow wobbles
Higher D to smooth changes
For acro flying:
Lower D to make sharper snappier movements
You will have to accept a compromise of optimal settings for stable hover and your typical mode of flying. Obviously factor it towards your most common style.
Other factors affecting PID
Taking known good PID values from an identical configuration will get you close, but bear in mind no two MultiRotors will have the same flying characteristics and the following items will have an impact on actual PID values:
Frame weight /size / material / stiffness
Motors - power / torque /momentum
Position - Motor-->motor distance
ESC / TX - power curves
Prop - diameter / pitch / material
BALANCING
Pilot skills