It is normal and expected that the response of some of the MODIS detectors will degrade over time.  Due to some hardware issues with Terra the response of some of the detectors have degraded at an accelerated rate.  The MODIS calibration team analyses the changes in response over time to adjust the calibration of the sensor.  The calibration changes are applied to the data so that the final products should only be minimally affected by the changes in response.  One main reason it is taking longer to create the Terra collection 6 products is the greater effort required to correct for the changes in response to properly calibrate the product.