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Challenges
The main development challenges with MCUs lie in the relatively limited resources that are available. Especially with the small, low-pin-count MCUs, you have to have a good idea of how many resources (CPU cycles, RAM, and ROM) a particular piece of code takes up, and whether it's realistic to add a specific feature.
This also means that picking the right MCU for a particular project takes both technical knowledge and experience. The former is required to pick an MCU that will suit the task; the latter is very helpful for the optimal MCU and helps to shorten the time that's required to make a choice.