Why does Arduino use USB A-B plug, instead of A to micro USB plug?
Please note that this answer is based on speculation and some common sense rather than on insider information:

If you take look at the hardware index, you'll notice that significant parts of the layout (drill holes, pin spacing, and position and type of the USB jack) haven't changed between the Arduino Extreme and the current Arduino UNO R3), while other improvements have been made. For changes between the UNO R2 and R3, please see Arduino UNO FAQ at adafruit (link provided by jfpoilpret).

It is thus reasonable to me that keeping the USB jack was a deliberate design decision: Improve if possible, but keep the layout changes to a minimum and allow for maximum backwards compaptibility.

But again, this is just the guess of a user!