[Ginto8]

To me, dealing with limit switches is a problem internal to the Subsystem - if it had to be dealt with by Commands, it would make every one of your Commands more complicated, which to me seems like insufficient abstraction. As for how to do it, I'd probably do something similar to how WPILibJ's PIDController works - use an internal TimerTask or Thread to handle the checking and overriding. That way, it doesn't matter what the Commands try to do - the Subsystem simply won't allow it to go beyond the limits.