I'm standing behind the individuality theory.
When the clones were first deployed, you see that they all were almost identical without separate markings, with the exception of the leadership and specific units/squads/Legions. While clones were 100% identical (with the exception of the ARCs and RCs), they lacked the individuality, which they gradually learned through their time spent in combat with the Jedi, which is easily said to have influenced the clone's mentalities and sway them into self-identification.
Fast forward, the "clone wars" as we know it are over, the Jedi are being hunted down. You could say order 66 was a programmed order to execute the Jedi's while at the same time "clicking" the clone's minds into a mental conditioning state to that when they are first grown and trained, hence, reversing everything they learned from the Jedi (now seen as the enemy) in regards to individuality. Since the influence of the Jedi is no longer present, the military forces have also lost everything the Jedi taught.
With the addition of non-clones, you have stormtroopers who came out of period after the jedi, so the general knowledge of the Jedi to the population is limited, given that records and histories have been restricted or erased by the Empire. I think all of these factors play into why they no longer have markings of any kind.
Though, we see in the Force Unleashed games, the individualized troopers, stormtrooper commanders, Nova troopers, etc. While not 100% individualized, they still stand out to represent their unit.
To add to the general population's knowledge of the Jedi, it's also widely known that anyone who speaks/researches or attempts to train as such, can find themselves in some serious trouble with the Empire. It may also be that those who do wish to individualized their armor externally could be seen as a form of dissent within the ranks which would fall in line with the Jedi's teachings, therefore, being illegal in the Empire's eyes.