Hi,
I would always go for a seperate MCU based FC with a companion computer for many reasons.
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Freedom of choice: You can choose both components to your liking/needs. Navio only works with a Raspberry Pi and the Emlid OS image. Same goes for periphals like GPS. No chance to change to a modern chipset with a Navio, except connecting it to the only UART.
If you need a companion computer with more processing power or just another OS (ROS on Ubuntu i.e.), you are stuck with RPi and Emlids Raspbian OS. -
Connectivity: A MCU based FC has more possibilities to connect further components. More UARTS, some have CANbus etc.
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Ease of use: Everything is much easier to do with a MCU FC. Firmware updates take seconds. No fiddling around with network interfaces/wifi settings/ssh sessions to just connect to the FC. Navio has no USB client mode and no preconfigured hotspot. A web gui for all the settings, reboot, etc would have also been a good idea.
With Navio you have to know something about Linux, networking, remote access, file operations, use special Navio related config files/tools all just to get a working FC. I answered countless questions regarding those topics over at the Emlid forum. -
Reliability: The chances of something going wrong on a computer based FC like the RPi/Navio combo are much higher. Even it is just a corrupted SD card, you got no FC and no companion computer. There is still no proper way to shutdown the RPi/Navio combo, except through a ssh connection. Every hard power cycle might corrupt the SD card.
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Support: The Emlid Raspbian OS image has not been updated for over a year. Their argument is, the user can download and copy new Ardupilot versions by themselves, if they want to use “less stable” versions. All links to the Navio2 have been removed from the emlid website. You can still find it in the store, but there is no link to the Navio documentation. They made a new site navio2.emlid.com, where you can find the links to the documentation. I do not get, why they hide the documentation like this, given that the Navio is a relativly complex device to use.
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Personal experience: I never had a Navio2 perform the same as a MCU based FC. GPS reliabilty was always lacking. Compass calibrations would fail, while they worked without a problem with a MCU FC on the same vehicle in the same spot. Corrupted SD cards just after arriving at the field, because the of an accidental power cycle during lipo connection.