It is a process that depends on lot of factors,
like –
[Input/Output state diagrams]
what are the applications of the project/device, what is input given to the system n what is the output desired

[Physical requirements and features]
from that decide what all data is required to be processed, number of GPIO to be used , redundancy for security etc. There can be multiple data sources so all basic sources of data to be thought through at this point.

[Transmission protocols – data n network as per application]
Next think of – from where n how to fetch the data (Communication/ interface), it covers all protocol needed all wired n wireless.

[Note : below mentioned is the difficult task n required patience ]
[Memory requirements and considerations ]
Next, think of data management, what data is required to store , what not (e g. – initialisation data, any used buffer that’s not required etc should be removed),
Where to store data : on the device or on the cloud or any remote server as per requirement.

If it is a real time system or a multi- threaded applications then here comes RTOS n multithreaded applications which require lot of synchronised processing.

[Power Requirements]
Lastly think of Power requirements, more processing n longer range of data transmission would required more power.

[Compliance n regulatory]
Also consider the industry/ stream it is being targeted to i.e. medical, consumer, industrial, defense etc. Accordingly there are ISO n IECs related to the part of application of project which is required for certifications purposes. Also there could be any region specific regulatory guideline that could be considered if going to hit the market.

Advice:
If going for a POC go for high specifications development boards which cost a bit more and cost cutting can be done later saves a lot of time.