I think if that was true Leia would never have made the comment about Luke being "a little short" for a Stormtrooper.
So all the height requirements in the earth militaries of history mean they were all Clones too?
Height requirements for jobs in the military haven't been that uncommon. It could be simply the Empire doesn't want tiny guys to be their "shock troops", since the intent of the "shock troop" (at least visibly) is to instill some fear.
That said though, Leia hardly was serious... It wasn't like she said very suspiciously, "Aren't you short for a stormtrooper?", like she was surprised. She was making fun of him it seemed, thinking he was just another goon coming to bring her to Vader or something, and Luke is quite short, so it's a moot point I think anyway.
As far as genetic material degredation, I think that's pretty common, but I don't know much about it... They did say they kept Jango around for that though, and Boba is a Clone so he's not exactly the best option either. Same with growing more samples. You cannot replace the original perhaps, which seems plausible since they were hanging onto Jango and "paying him a considerable fee" to do so. Why bother if you can just scrape the fingernails of any random Clone?
The Empire surely wouldn't want infiltrated by Rebels, but it still happens. Clones or not Clones, it didn't seem to matter, so again that's not really a solid argument for or against.
I'm sticking with the simplest argument then... The Empire's described as "a million million worlds", and at ROTS's end, it seems like quite a popular idea among the majority. "This is how liberty dies, with thunderous applause". The people LIKED the Empire idea. They liked what it offered. There would be a trough of individuals ready to jump at the chance to serve it if it's so popular. Hell, there were probably already enough to serve it during the Clone Wars, they just used Clones because they're perceived as dispensible during a war, whereas recruits are not... When the war ends, those willing to serve would likely increase by quite a lot, especially when everyone loves the ideas the Empire was feeding. "Freeing the galaxy of tyranny, making life peaceful and prosperous", and so on.
I'm not totally opposed to some Clones still being on-hand, but I think the vast majority of the Empire is made up of recruits. It's what EU's supported, and it's even supported by the films somewhat, so I'm sticking with that. I love the Clones from the era they're from, and how the "Clone Wars" is talked about like that was a long time ago, and those things don't go on now... Otherwise I suppose they'd call the war with the Rebellion the 2nd Clone War, rather than the Galactic Civil War.