For instance was Cody better than normal Clones?
I would say simply a clone commander would get more training specifically in battlefield commands. So example typical clone takes 4 years to be battle ready, commanders would take 6-8 years with additional schooling.
our second option is that there is deviations with the clones and some are smart, faster, stronger then others as the same genetic material can have options (this is less likely since the fact that they seem to have perfect manipulation of genes) these better skilled clones are given the commanding positions.
Yes and Yes.
It all depends on specialized training and experience. Identical hardware can't necessarily make two clones same. Every clone has his own personality and skill level. See answer to a similar question: Why was R2-D2 smarter than other similar droids?
Take example of Cody (CC-2224) from Wookieepedia:
In the beginning of the Clone Wars, CC-2224 was a captain, but when General Kenobi saw his skill, he recommended the trooper for a promotion. CC-2224 was then made a marshal commander.
Initially, Cody got captain's training (leadership skills are important here). There are other skills like sniping etc but it doesn't require you to think for others. So, a captain surely is tougher by specialized training to make strategies and to command more than one.
Later, he got tough battlefield experience while with Kenobi which made him even better. And then, he got promoted.
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.
I wouldn't say so much that they have different "abilities", as they have been given different training. In the conversation with Obi-Wan on Kamino, Lama Su (the prime-minister of Kamino) states:
We take great pride in our combat education and training programs.
Just as some clones were likely trained for battle on certain types of terrain (desert, forest, swampland, etc.), and some were trained with specific weaponry, some clones were likely created and trained specifically for command positions within the clone army.
There is also the individuality of each clone. While they were created, trained and "raised" in the same environment, each clone would still have had somewhat unique "life experiences" that would affect their thought processes as they went through their training (e.g., Bob tripped over that twig and the rest of his squad made fun of him for it... Bob never let go of his embarrassment over that incident, and is always striving to keep from making a stupid blunder like that again). Lama Su also stated:
I hoped you would be pleased. Clones can think creatively. You'll find that they are immensely superior to droids.
Their ability to think creatively also plays into this as each clone may come up with a different solution to the same problem. Some may fail where others succeed. A failure may result in a penchant for hesitation, whereas a success gives a bit of an ego-boost in future tests.
Yes. Some clones were even genetically enhanced, such as the Null ARC troopers. It is perhaps better to think of Jango Fett as the baseline from which the Kaminoans created nearly cloned individuals rather than a perfectly identical clone template. In fact, all the clones except Boba had genetic modifications from Jango's baseline:
Lama Su: Apart from his pay, which is considerable, Fett demanded only one thing - an unaltered clone for himself. Curious isn't it?
Lama Su: Pure genetic replication. No tampering with the structure to make it more docile... and no growth acceleration...
Star Wars: Episode II Attack of the Clones
Anyone who knows identical twins knows that identical genetics is not the same as identical people. It's inevitable that the clones would have different personalities and aptitudes in addition to their specialized training.
epigenetics- literally translated above genetics
even two genetically identical people can have different physical and mental traits based on which markers are turned off and on and 99% of epigenetic markers are flipped by the environment your in. so giving different supplements, and conditions (or just flipping the markers via tech ) can produce two different people even though there base code is the same.
couple this with training differences and boom two cloned people who are way different