So why doesn't the Empire use them whenever possible instead of stormtroopers? Is there an in-universe reason why the Deathstar isn't carrying clone troops or why a backwater world like Tatooine isn't left to mostly droid troopers instead of human stormtroopers? While I can understand why one would not want a 100% droid army, it would make sense to use droids when possible, since they don't need food (just plug 'em in), parts are interchangeable, and they're even more disposable than clonetroopers are.
So when the Clone War is over and Sidious is in control of everything, he could easily obtain the battle droids the Separatists used without much trouble and a minimum of expense.
The Separatists were under control of Count Dooku, who was under Sidious' control, who was essentially running the entire Clone War and using it as an excuse to take over the Republic and turn it into an empire.