Yeah, this is my least favorite feature of the K-3. (I've been lucky to not have any mirror flap issues, not sure if it is my camera or that I vigilantly watch the battery's power level and change sooner than I would have on my K-7)
Moving my right thumb to click the AF-point select button is not so nice. Its just not so fast as the old K7 method of using the OK button in the 4-way control to toggle AF-point selection. In my hands, it feels much less ergonomic. It reminds me of how my thumb has to bend significantly to use the keypad on my Samsung phone- cramped. In addition, I think the grip when using the OK button is much more solid than the new 4-way control. Much rather have the option to:
a) disengage that button entirely for AF-selection
b) use the old K7 method (press the OK button to toggle)
c) use the Fx button. This method would be ideal for me as I don't really care for any of the current Fx options and I always shoot RAW or RAW+, so I don't have any use for it as a RAW button. Moving my thumb from the side of the lens barrel to the Fx button is much more natural and allows the rest of the hand to cradle the lens. Besides, it would allow me to keep a very good grip on the camera body along.
A firmware update should be able to give us these options.