My answer to Why are the pins of many MCU's separated "randomly"?
Answer by Shaunak Agastya Vyas:
That is because of the IC Manufecturing method. The VLSI of the IC happens in such a way that it is difficult to place the same-port pins together. So many electrical and elcectronics theories are the causes.
For example, if Pin 1.0 is PWM pin, then Pin 1.1 may be ADC pin and Pin 2.4 may be another PWM Pin with the same channel as 1.0. So they place 1.0 and 2.4 together in order to crunch hardware.