Basicamente, quando Palpatine transformou a República no Império Galáctico, ele renomeou as tropas clone para os Stormtroopers Imperiais.
Do Star Wars Wiki em Clone Troopers :
In a prolonged speech regarding the downfall of the Jedi Order and the end of the Clone Wars, Palpatine announced that the Republic would be supplanted by a New Order; the first Galactic Empire, in which he would rule supreme as its first emperor.
Just as the Republic was renamed and reorganized into the Empire, the clone troopers were also affected by Palpatine's reforms. No longer known as the clone troopers who defended the Galactic Republic under the leadership of the Jedi Order, the clones were anointed as Imperial stormtroopers.
A Enciclopédia de Star Wars declara que " eles [stormtroopers] não recebem mais orientação do sabedoria dos Cavaleiros Jedi. Em vez disso, os stormtroopers são empregados nas mais brutais ofensivas imperiais, comandadas por oficiais e governantes cruéis. Isso pode explicar por que eles se tornaram menos organizados.
Alterações na cor e armamento são simplesmente atualizações. Após o rebranding inicial como Storm Troopers, os antigos clones ainda teriam suas armaduras coloridas. Mas novos lotes de clones foram feitos com armaduras melhoradas e, eventualmente, os antigos clones de Fett morreram em batalhas, especificamente na Batalha de Kamino (Star Wars: Battlefront II). Do wiki :
At first, the Stormtrooper Corps was composed almost entirely of clone soldiers based on the Fett template. That included the remaining clones that were engineered on Kamino, supplemented by the millions of clones created on Coruscant and Centax-2 through Spaarti technology, and three new stormtrooper clone batches grown in the Outer Rim Territories. During this time, traces of the clones' obsolete armor remained in the design of their new and improved armor. However, the stormtrooper ranks would cease to be dominated by Fett's progeny after the Battle of Kamino in 12 BBY.