Hi,
What you have to realise is that the I/O pins are just that, they can be assigned to be input or output, analog, digital, I2C, UART, PWM, Comparitor, Reset, Vref, and other functions.
Having a permanent pull-up or pull-down may inhibit the performance of some of those functions.
Some devices that would be connected to the controller ICs input, may not like being loaded with pull-up or down resistors.
Good to see you did some research before making your queries.
Thanks.. Tom.. 