KOTOR1 was an utterly enthralling experience the first time through, but having played through it twice more I can see the boring stereotypes present in most of the characters, the moments of boredom and poor design, and the ultimate banality of the story itself. Whenever I think of it now the first adjective that pops to my mind is "entertaining", and not "great".
Morrowind, during my first play-through, struck me as a fascinating, frustrating mess of a game before I began to understand and appreciate it's unique style and pacing - of course the story moves along in fits and starts, that's what it would actually be like to be that character, who had to make a living in a dangerous, difficult environment at the same time he/she was following Caius's orders and gradually discovering who he/she really was. By the time I slew Dagoth Ur I thought it was without doubt one of the five greatest games ever made, and my opinion hasn't changed with subsequent playthroughs. But I will admit that much of my opinion of Morrowind's greatness comes from the way I interpreted the main story. As an atheist, I interpreted the creation of the Tribunal as a rebellion against the order of the universe, that reduced the mortals of Tamriel to the playthings of the Daedra Lords and the higher gods, who were personified by Azura: the most "benevolent", but also the most manipulative of the Daedra. I still believe that Vivec's actions were ultimately noble, even if he did have to betray and murder Nerevar to accomplish them. So I saw the destruction of the enchantments upon the Heart of Lorkhan as a tragedy - the Tribunal, the great bulwark against the divine, were cast down, and humanity would be slaves to the gods again. It was sad, and I was moved.
Sarafan, you're wrong about KOTOR II, but I admit you have to be very forgiving (or really like plodding, dense, cerebral games) to really appreciate it. If it was a mess, well, if Chris Avellone had been forced to release Planescape: Torment before it was finished, it would have been a complete mess too, and I think that the ideas presented in KOTOR II are more interesting than those of Torment. The story's not about the Sith Lords. It's about the Exile.