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No one use Arduino microcontrollers anymore. Teensy antiquated Arduino a long time ago.
Kind of... AVR processors are garbage. They really aren't much cheaper than a 32 bit ARM processor and they've got less RAM, FLASH, and speed. But, Arduino has several different processors that are supported - AVR, SAM3X, etc. Teensy 3.5 and 3.6 are very nice boards and I do like them more than even the Arduino Due. But, they're pretty close to an Arduino Due and which you choose is kind of down to what you want to do. At any rate, both tend to be programmed from within the Arduino IDE and use the standard Arduino API. This allows one to get into the use of these more advanced boards with minimum hair pulling.

For the op - I'd recommend the Teensy 3.6. It has CAN which you might need (though you must provide your own CAN transceiver. When in doubt use SN65HVD234) and it has an sdCard slot built in. This gives you excellent logging capability. You'll have to make up an adapter board that the Teensy plugs into. That board should have connectors, the CAN transceiver, and any I/O drivers you might need (optoisolators for input, transistor outputs, etc). But, the Teensy 3.6 is a great place to start.
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