Well, The Matrix is a whole other can of worms with me, as I really like them, all three (well the third one is flawed, but the second is a LOT better than how it's treated). But let's not talk about that.
As for Star Wars, it sounds like we don't disagree so, so much. Plot holes were a consistent problem, originals, prequels, and gap between prequels (man did Obi Wan age!). I guess I was vaguely more interested in the intrigue of the prequels--Anakin's slow turn to the dark side, Palpatine's nefarious take over, there's some mystery in II--than running around shooting guns at comically inept guards on the Death Star, or Ewok Forest.
I will grant you that characterization and acting is much better in the originals. Hayden Christiansen and Natalie Portman give the flattest performances of their lives in the prequels, matched only by the shoddiness of the writing.
But the effects of the prequels blow the originals out of the water. So it just ends up being a bit of a mixed bag for me.
Don't get me wrong, I think there are a lot of great moments in the originals. I agree with you there. I could watch Luke, Vader, and Palpatine all day. But then there are teddy bears knocking down giant armored robot tanks with bamboo spears. Mixed bag, like I said.
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But compare to Lord of The Rings. Now that's a perfect movie trilogy.