Now, according to the films of the Original Trilogy, there is NO origin given for the Stormtroopers. The viewer is left to assume whatever he/she wants, or like me, you can turn to the EU. Fine. Good. Then, Episode II comes along and we learn of the development of the clone army. At this point, the viewer knows that they aren't really going to be used to defend the republic, we know that they were created at Palpatine's wishes.
Enter Obi-Wan... standing on the balcony and looking out over what are, UNDOUBTABLY, the Stormtroopers. They don't just look similar to Stormtroopers, they ARE the Stormtroopers... albeit known to the Senate as the "Grand Army of the Republic". Sounds fancy, doesn't it. I'm sure Palpatine thought so too. The Republic sure dug it. "Awesome" I thought... Lucas' design for their origin trumps the EU, and in this circumstance, I'm glad.
In the EU, the clones have been rendered largely obsolete and replaced with a standard Human army.
In the films, the clones ARE the Stormtroopers.
So, which one can you possibly side with? Some would argue to just pick whatever story you like. I say that the EU has created a discrepancy with narrative of the films, and must be overridden. Retcon the EU, or whatever, but the Clones ARE the Stormtroopers... This is Lucas' design. He has ignored the EU on several occasions, and has done so for the Stormtroopers. I must side with Lucas.
To address your points:
1st, I wouldn't exactly call an army that can erradicate the Jedi "Stupid" or "Insignificant". The Death Star has one function: Destroy planets who don't tow the line. The Stormtroopers were the first line of attack in "convincing" disgruntled systems to shut up. Because the Death Star is "Plan B". Everything rolled into his lap because of the grand design of the Sith to defeat the Jedi. Yes, the whole pie was HIS... now he would have to keep it.
2nd, Honestly, I'm not exactly sure what you meant here...
3rd, The Clone Commandos who disobeyed Order 66 were largely ARC Troopers, and even then the percentage of total troops to disobey were easily less than 1%. If this made him nervous, how would drafting strangers improve loyalty? How could you know his personal motives? The Clones had NO ulterior motives. The Clones were totally obedient. Obedience to their leader was part of their genetic design, according to the Kaminoans.
Hence, the Purist trump card: "Only the films are canon"