I own a MultiWii pro (not the one from RTFQ) and 3 KK2.0 boards.
The RTFQ boards take the flashing and Arduino learning curves out so they are a better board than the MultiWii pro from HK.
However, the MulitWii Pro will add two additional variables to your build and tuning.
You will need a device with which to program your board such as a computer, laptop tablet or if you enable BlueTooth a smart phone. This is needed for a MultiWii to set PID, on board expos, set magnetic north, calibrate sensors, etc...
If your device is not mobile, modding PID takes time.
Also, you will need to accomodate the USB port on the side of the MultiWii in your build. If you use a FT frame where the board sets in the frame for protection, you may have to mod the frame or move your board to be able to connect to the board with the USB connector. You MUST accomodate that USB connector in your build or you cannot program the board without BlueTooth.
The KK2, has no GPS. It has no return to home or programmable trips. It just flies the copter. If you don't pay attention while you are flying you will crash even in autolevel mode.
It also doesn't have any parts that hang off the side or connect to it from any other angle than from the top. With the KK2.1 you tune the copter in the field and need no other device.
If this is your first multi-rotor build (not just your first tri-copter), I recommend you keep it simple, and light. The KK2.1 is far simpler to work with.
If you are a seasoned flyer and have no trouble adding Blue Tooth or have a ready laptop or tablet and have no issues with accomodating the MultiWii, buy the cover RTFQ sells to cover the board and the sensors and get a GPS module stand for your copter.
I also use a Turnigy 9x and have no issues and the gyros and accelerometors and the barometer (which you need to cover) are integrated into the board. Welcome to MultiWii land.