This is just my own two-cents, but even if Sauron had the power to dominate the dragons, do you think he would? I imagine he'd be slightly miffed at them, considering some of them had consumed some of his Dwarven rings. That fact alone would have had him attempting to completely enslave and torment them, if he could, but since he didn't, it leads me to believe that either their usefullness slipped his mind (such as the existence of hobbits once did) or he didn't, at any given time after Isildur took his ring, have the power to, and thus left them alone to pursue more important matters, like the finding of his own ring which would give him the definate power needed for world-domination. I prefer to think that he was too busy to deal with the dragons.
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