The units fight a lot longer, and you don't have all that chasing of routers over the red line. The elephants threw people all over, but eventually went amok and many elephants were killed. The Cartaginians still won the battle on medium difficulty. I think you could leave fatigue on and still get the longer fighting. You could also leave limited ammo on. It's morale and routing that is causing the quick resolution in the fighting.
I didn't try increasing the command rating on the generals, but you might get the same effect that way except if the general dies you will loose. I did try playing with the melee units boosted to experience 8 in a mod with larger units which does raise morale, but it didn't seem to raise it enough to lengthen the fighting enough for me. A flank hit by cav would still send a unit packing, and then all the other units would tend to rout very easily. If you want it to be over when the first unit routs, then leave morale on.
Turning off morale does reduce the effectiveness of flanking since you can't trigger the rout, but it introduces the tactic of using reserves to counterflank or plug holes in the line.
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