I wrote a post on a method to organize Raspberry Pi GPIO so that it acts more like a controller than just a single board computer with I/O. To summ...
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You may be looking for something more simple, but did you know you can run many industrial PLC runtimes on raspberry pi, such as Codesys and Axel LogicLab, amongst others.
No, I didn't. I am looking for simple, but I am interested in other tech as well. Any wheel I don't have to reinvent is good. I'm several years out of the PLC industry, so my knowledge base there is behind.
Yer, it's pretty good. A codesys runtime can be brought for £50 but but it's easily prograable in any IEC language.
You can even get commercial products based on it too. Which then look more like PLC and have relay modules 24V etc so can slot right in as a cheap PLC. And you still have a pi at the heart to do anything else you want.
Such as:
Piextend
Revolution pi
Unipi
Controllino
For PLC type programming of arduino you could also check out soapboxautomation.com/support-2/so... that I stumbled on while researching Twincat...