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I agree that "reserve unused pins as outputs tied to ground" could cause problems and probably shoulnd't been choosed as Quartus default option by Altera. But I think, it doesn't touch pins assigned otherwise. The issue is with pins having a particular hardware function but are yet unassigned in Quartus design. For this reason, I use "input with weak pullup" option (but sometimes, I may forget to change the option).
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The default is better for new device families. For a new Cyclone III or Stratix III project in QII 7.2 SP1, the default is "As input tri-stated with weak pull-up resistor".
I prefer "As input tri-stated with bus-hold circuitry" so that the default is suitable for unused I/O grounded on the board without wasting current through a weak pull up.
If your preferred project-wide default isn't suitable for all pins like a few that are grounded on the board, change the setting for individual unused I/O pins by using the "Reserve Pin" setting in the Assignment Editor or Pin Planner.
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