There are two reasons I don't like to rotate my punches over with bare fists.
Firstly, You don't get the low elbow power. The closer to the center of mass your elbow is at impact, the more mass you can drive it with. There are of course stylistic exceptions to the latter point, such as if your power comes from body rotation, IE swinging it like a bat on a circular line, but thats not too applicable to(most at least) styles of WC.
Secondly, it's much easier to break your hand or injure your wrist if you over rotate. This is not so much the case with boxing gloves of course, but that's a whole different animal.
Edit - after I posted a third reason occurred to me. Rising power. Two of the most valuable things I got from my WC were the concepts of rising power and sinking power. Sinking power is something that is more situational for me, but all of my straight shots draw from rising power, ie, slightly coiled legs and torso that combine with the hip rotation and arm movement to generate more force. If you rotate you break the line of power from the ground.
Ill whip up a quick video to demonstrate what I mean.
Second edit -