I will agree completely on the fact that when you watch Star Wars you can see the mythological references as well as historical references (cant remember if you said that but anyways) as with comparing that to LOTR, it isnt really fair for that on the the terms of refrences.
LOTR was pretty much ripped straight from (and I will need to check this) norse mythology. Where as Star Wars combines multiple mytho with historical events like hitler and what not to create such a great story.
But enough about mytho and that this is a Star Trec forum haha 
Now Recently I did sit down and watch all the Star Trec Series and when I say everything I do mean everything.... and my god. Now sitting aside all the time I spent the episodes that you pick out that you remember, I agree 100% on them they where fantastic! But like you said the down side is pretty much all the random episodes that come for every one of them episodes which kinda stinks but it was someones childhood.
Now for all the Trek movies Khan was by far the best in my opinion. Now this doesn't include the newly released Trek only because well I point it towards your previous "ravings of that creepy homeless guy who stands outside the Starbucks and smells like mushy peas for some reason"
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As with the final point of your post of Star Wars being a book a long one that i refuse to count the first three chapters, where as Star Trek is a collection of stories. I can agree with both points of that and this is what makes it so hard to figure out which one is better, on one hand you have a Book that people that connect to because of all the ties into history and mytho, where as Trek has them really great episodes and movies and characters but its much harder to connect to for some because it really does kind of walk that line of sci fi or fantasy. ( I think it was you who said that in a previous post not sure thou)
When it comes down to it, im sure that this debockle will come down to ryan and dork doing some spoof of lightsaber vs phaser. 