Is there an explanation of why the clone troopers changed to storm troopers? And why the clone troopers seemed to be more organized and specialized (colors, weapons variations, etc) than Storm troopers?
Basically when Palpatine turned the Republic into the Galactic Empire, he renamed the clone troopers to Imperial Stormtroopers.
From the Star Wars Wiki on 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.
The Star Wars Encyclopedia states that "they [stormtroopers] no longer take guidance from the wisdom of the Jedi Knights. Instead, stormtroopers are employed in the most brutal of Imperial strikes, commanded by cruel officers and governors." This may explain why they have become less organized.
Changes in color and weaponry are simply upgrades. After the initial rebranding as Storm Troopers, the old clones would still have had their colored armour. But new batches of clones were made with improved armour and eventually the old Fett clones died out in battles, specifically the Battle of Kamino (Star Wars: Battlefront II). From the 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.