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We decided to use the Jaguar because even with the loops on the CRio, you must put in a delay of some sort ...
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This implies there is no delay within the jag.
I would think the major control difference would be that the Jag runs the PID at 1KHz and the PWM signal can change the motor speed no quicker than 5ms, or at 200Hz.
The capability of doing control on the Jag is cool, but unless your flywheel is very light, I wouldn't think that the control rate needs to be 1KHz. So you should be successful doing it either way.
Greg McKaskle