There is no empire to train them. Clone troopers were trained by the good folks on Kamino.
When the Empire is finally restructured and the start of the Galactic Civil War actually begins, the Clone Troopers are absorbed into the Stormtrooper Corps which is a majority human recruits and other clone templates.
Lucas had an idea about the Clone Wars long before the prequel trilogy came about. They might have superior traits, but that doesn't mean the have the skill of Jango Fett.
Also, cloning troopers is likely cheaper due to their accelerated growth. Such that, in only a few years, you could raise a massive army without salaries, pensions, etc.
In the prequels, the big sticking point about the clones was that someone was building a secret army to start (and potentially win) a war; and that this person was a Jedi claiming to work for the Republic. This lets you, the viewer, know right away that there is a nefarious plot to very likely overthrow the Republic (if you didn't already know, lol).