As for Stormtroopers, I'll always see them as elite troops, the emperor said they were his finest legion of troops on Endor, the Tantive IV, and all sorts of other examples.
Sure, he says that, but look at their actual performance as shown on the screen. On the Tantive IV, sure, they did fine... in that they blew ONE entrance into a ship during a boarding action, then shoved numbers through that hole without any cover (really, that should've been something the Rebels could've held against for much longer - neither side fought well there). Even today, an action like that would be started with some kind of grenade being thrown in, likely a flashbang or other concussive grenade if you wanted prisoners, and you'd definitely come in from more than one access point to prevent focused fire from plugging the hole (which is what should have happened but didn't because movie). On Endor, that legion of his best troops takes prisoners without restraining them in any way. Then that legion is ambushed by primitives firing weapons that are literally bouncing off their armor... and they scatter, immediately abandoning the fortified position that they are there to defend (and those unrestrained prisoners) to chase in small groups or individually those primitives into the forest. This is NOT disciplined, highly trained troops at work. The only time stormtroopers are actually competent during combat in the movies is the Hoth assault, and that is largely mechanized; we see little of the stormtroopers directly in action, except for their notable failure to stop the Falcon from taking off.
Again, I LOVED the EU deciding that stormtroopers were actually elite troops, and coming up with ways to explain away their poor performance in the movies. The Hand of Judgment, for instance, was an awesome group that kicked serious ass. But those explanations are all after-the-fact, and at best are barely hinted at on-screen.
I just always thought of the Empire as the perfect military force, including ground forces and what not. What got them was incompetence and what not of the Emperor and stuff like that - not to mention the various plot bunny attacks.
Again, look at TIE fighters, the basic TIE/ln. This is the primary fighter of the Empire and yet, by most standards, it is not a good fighter. It has no shields, no hyperdrive, it has only two lasers as its armament, and it's not even much faster or more maneuverable than other fighters on the market (hell, it didn't even have a life support system). The one thing it had going for it was that it was cheap and easy to mass produce - and the Empire didn't care about losing pilots, because it had so many other people to replace losses with. Contrast that with the clones' V-19 Torrent, which had lasers, shields, missile launchers, hyperdrive ring compatibility and was one of the most maneuverable fighters of its day, or with the ARC-170, which had shields, torpedo launchers, internal hyperdrive and a rear turret.
The Empire's military was purely a quantity over quality machine. The TIE Interceptor wasn't introduced until after the Rebellion started and Rebel fighters kept kicking the snot out of TIE/lns. Other advanced TIE models were flown almost exclusively by officers and VIPs, but the normal pilots? Most of them ended up dead within a year or so, and mostly because their equipment was shit.
Despite this, you are still right in that the Empire still largely lost because plot bunnies + arrogance/incompetence of the leadership.
I can agree with your whole thing on clones having heart - they do, but in the end I always believed that they thought it was their duty and job to kill the jedi fro the republic.
They did. They just didn't know it until the order actually came through. They were not created with the conscious knowledge that this order was there and just waiting to be implemented, but with this order buried in their subconscious, just like many other orders that, once given, they would have obeyed with equal lack of hesitation. This is the conclusion that everything shown on screen points to, and since modern Star Wars stories are only counting those things that were on screen or in the NEU, that is what we've got to work with now. However, I've read very little of the NEU, so if something in there contradicts me, take that over me.