There is no reason, why you should not use your own communication for yourself.
There are so-called "Standards", communication layers that everybody can rely on. This makes our life easier: there is an UART, I may use this UART and I can connect to somebody elses UART without any getting any problems. PSoCs rarely introduce new communication paths (CapSense is one for man-machine-communication) but implement the industry standards as UARTs, I2C, SPI and so on. So PSoCs are able to communicate with thousands of "alien" chips which are using one of the standards as well.
An additional thought, newer scopes have protocol analyzers in them, so makes troubleshooting
an issue in a design easier. If you have a "custom" protocol, no one can easily set up for a diagnosis.
Standards are good.
However, sometimes for competitive reasons, you might forgo the prior, thats a decison only you can make.
Lastly you may not care about pin count, but you can bank on a major customer walking thru the door and
asking for just one more set of pins for more capability, and he wants the design variation yesterday. So
todays serial interfaces are great, USB in particular, to conserve GPIO. Just one more variable to make
us all crazy....:)
No, there is no reason why you cannot use your own protocol. But as state above, that there are tons of tools and application using standard protocols and it would be much easier to interface other device thru standard interface.
For paralllel interface, you should check with the centronic interface used in the centronic parallel port ( printer port for PC). Using a COMMON protocol means you have device aviable and also others with the experience of those interface can help without needing to learn your interface.
Those "standard" were there, why re-invent the wheel, when you can desingn your own car?
If you are designing somthing specific or something new, then it is another story.