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What exactly is the application? There are more then one criteria like cost of BBB is more then RPi3B other is BBB has separate unit called PRU which at times becomes very handy. Then BBB has onboard EMMC storage but that's not the case with Rpi.
The RPI should not be compared to the BBB, being the RPI3 a better candidate in terms of performance and price, whose cores are very similar, and judging by its interfaces, apparently the RPI3 is purposed to be used in local applications whereas the BBB has what would be expected of an embeeded system as its quick boot and NAND memory; the fact that the RPI`s SDcard can be easily removed means a weakness in the sense that it can be easily cloned;
Another aspect to be considered is that the RPI baseline has a community somewhat wider than the BBB, which ensures in a way a greater support for any problems that you find, since surely someone had experienced the same and could give you tips for solving it.
Both are great platforms, somehow similar, and at the end you will decide taking into account one or other small detail.
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