I tend to think the real flaw was in pretty much the entire Clone Wars and clones-as-troopers storyline. It never made a ton of sense to me and always seemed at once convoluted and disjointed.
Not necessarily though, as Palpetine clearly had the resources and the available technology to carry out his plans. It was made clear to Obi-wan that the entire clone army was a complete surprise and unknown to them. It was the quickest method to build an Army and maintain complete control of those within it's ranks, hence, "Order 66" was established with clones with complete and total loyalty to his command, therefore enabled him to kill off a good number of Jedi, while taking complete control at the same time.
Simplifying it, it was because:
-Completely controlled development and creation of an entire army
-All clones means no conscripts or any issues that comes with enlisting others
-Completely done in secrecy
-All the clones are identical, that means that after the genetic re-configuration and aging control, medical and physical attributes are modified, essentially every clone wears the same exact sized everything, eats the exact same diet, etc. which saves a considerable amount of cost associated with it