There are a few considerations that need to be made into selecting a microcontroller itself, rather than the dev board. Assuming the project contains fully custom electronics, there is no limitation on the exact MCU chosen as there would be if you were only selecting between dev boards. Students and hobbyists sometimes artificially limit themselves even further, sometimes staying loyal to certain ecosystems and only selecting from dev boards within those ecosystems (such as Arduino or mBed). While there is certainly nothing inherently wrong with any of the ecosystems, you'll fail to grow as a professional engineer if you're incapable of considering other solutions or appreciating the unique strengths each piece of hardware brings to a particular project.
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