Communication can be done in a number of ways. the methods include: Parallel – where several lines are all sending a part of the message at the same time (Imagine you want to send the number 1234. Parallel communication would have all 4 digits sent at the same time.) Serial communication has one line sending different messages at different times. (If you want to send the number 1234 it might send the 4 first the 3 next then 2 then 1.)
It is way more complicated than this. There are token rings, communication buses, phase modulated, watch dog timer synchronization,.. endless.
The architecture is carefully chosen to optimize the processor capability with the I/O needs of the system. Rest assured, every pin has been discussed and argued over by engineers and designers for many hours to come up with the layout we see.