"These settings will apply to the player's assigned position, not the position they would be in the lineup for. For example, if you have a linebacker in your depth chart as a defensive back, his fatigue calculation will use the linebacker's setting and not the secondary setting."
I've taken the above from the misc tab in the gameplanning page. In light of the amount of teams using players out of position, I think this needs to be reviewed.
As the rule is now if you convert a DL to CB and play him on the DL, his fatigue will take longer to run down. So not only does he get a speed/acceleration boost on the OL players he also tires slower causing the boost for speed/acceleration to be even more exagerated.
I think each player needs to have a 'stamina' setting based on health/condition and strength. Heavy set linemen should get gassed fairly quickly, Linebackers should be able to go a little longer and Secondary the longest of all - but, it should be based on the position they line up at and not the label on the player card.
I would suggest a stamina setting for each individual which is effected by physical contact in the position they line up at and the size/strength of the opponent they are in contact with.