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Any reason you decided to use the Arduino for this purpose rather than jsut connecting the encoders directly to the cRIO?
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We have included projects like this for the last few seasons to involve more students in programming for the robot and to add additional languages to our training program.
In most seasons we have about two students who really become the lead programmers for the comp robot. In order to sustain a larger group and have their work be meaningful we have added components like the Arduino.
We try to pick something useful yet achievable by a group of students with little oversight. Last year's encoder reading was a success, though we stopped using it before Worlds because of some unknown and possibly unrelated errors. Regardless those students were proud of their work and had a featured component on the robot that otherwise would not have existed.
In past year's, when we've had mentors with PCB design experience we have tried things like a hardware based PID board that used SPI to talk to the main controller.
This year we plan to use it the Arduino again, though the scope of the project isn't defined.