Difference in Genetics between some Clone Commanders and Clone Troopers
There is difference between some Clones even on a genetic level, in addition to the differences introduced by training and experiences.
According to Republic Commando: Triple Zero, the Kaminoans tampered with Fett's DNA to emphasize and alter certain qualities such as loyalty, aggression, independence and discipline; with the rationale that "an "unaltered" Jango Fett was not the ideal infantry soldier."
The ARC aka Advanced Recon Commandos was a completely separate variant of 100 clones, different from the general run-and-mill soldier, with high autonomy. According to Underworld: A Galaxy of Scum and Villainy, not all of these 100 Alpha-Class ARCs executed Order 66, in fact after that incident many of them left the soon-to-be-Imperial Army to strike out on their own.
Some of them held the position of Clone Commander.
Difference in Abilities between Clone Commanders and Troops with Identical Genetic variants
However, even among the general variant of the clone soldiers who had the same template, individual abilities and preferences and skills were seen. This is fitting because even in the same environment, paths of development can be different, as seen via twin studies; genetics is not everything.
As the best known example of a (non-ARC) Clone Commander, according to The Official Star Wars Fact File, Cody showed independent thought from early on in his training, which is what led the Kaminoans selecting him for special training. This training was where he met future Captain Rex, so presumably this was given to other clones exhibiting independence and meant to put them on the same track to promotion.
Then there was the ARC Training Program (set up by ARC Trooper Alpha-17, who also handpicked Cody for this training). This was an experimental officer training program for the general template clone troopers, designed to provoke independent thought. So, certainly it also seems that the individual capacity of certain genetically identical clones, was also something that training could enhance.
One of the Roleplaying Games, mentions the Commanders being bred with extra capacity for autonomy, tactical thinking and coordination, but there's no other reference to genetic variation outside of the Alpha-Class ARC Commandoes elsewhere in the EU, that I could find. Most fact files and the like only mention extra training, specially the ARC training for greater independence instituted by Alpha, as what made the Clone Commanders' existing aptitudes stand out and stand up to the test.
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