In many ways, yes, though I've seen it argued that the Aragorn/Arwen subplot is a distraction from the overall "Lord of the Rings" narrative and should be treated as something minor. I happen to disagree to a point, seeing as the book shifts focus towards Aragorn's ascent to the kingship in the end, and his relationship with Arwen is somewhat tied to that, but I've seen the argument made in a pretty reasonable and convincing fashion nonetheless. It's true, however, that the Arwen/Aragorn relationship is not vital to "The Lord of the Rings" and really serves to tie the book into the greater Middle Earth mythology and provide a grand, royal ending. This is why I only disagree to a point.

“The Lord of the Rings” is filled with such things, little pieces of story that support the whole narrative but which are not necessarily vital to, or even desired in, the main text. The history of the Mines of Moria and the people of Durin, for instance, adds greatly to the Moria sequence, but that information is tucked away in the appendix, too. Most readers will never see it. Or the full history of who Galadriel and Celeborn are, and why Lothlorien is the way it is. That's something that really needs some lengthy explanation, so the reader new to “The Lord of the Rings” would not fully grasp the tragic history of the elves, how they ended up in Middle Earth and of their long conflict with evil (as well as their often talked about but never explained passage into the West.) The appendixes add this stuff for people who want it without cluttering up the narrative with unneeded exposition.

The point I'm taking my time getting to is that these things, while these items add great depth and clarity to the story, they are not vital to the narrative and do nothing to propel the plot forward. Since the book is hobbit-centric, the reader (through the hobbits) wouldn't know much of this stuff. By having it there, half-explained, we are given the illusion (or shown the reality) of a much vaster history and/or layers of meaning beneath the story without getting in the way of the actual story. For the reader who isn't aware of this stuff, it makes everything seem bigger and vaster, and to the reader who is, it adds new layers to the tale.

(And to your initial question, yes, I think Tolkien could have handled the Arwen thing much better. In his early drafts he had Aragorn marrying Eowyn, which is the route I think he should have stayed on. It's a much more logical and emotionally appealing resolution.)

Tolkien made a number of comments on these matters in his later years as he struggled to bring the Silmarillion into some coherent form. Many fans liked the fact that historical events that are not clear to them are referenced in LOTR, adding dimension to what is for all intents another world with an actual history stretching from the beginning of the world. The Silmarillion and a number of other works that expand on it certainly gave greater insight into the history that drove the events of the Third Age.

No, not at all. In fact, the thrusting of the Aragorn/Arwen relationship to the forefront is EXACTLY what makes the movie trilogy (granted we've only seen the first part, but it's pretty clear where they're going that way) so different from the book. The movie is a Hollywood movie that is in some ways how Hollywood would have approached the events Tolkien wrote about if they had been real historical events. To Hollywood, the Romance between the Future King and Arwen Half-Elven, bringing back together the two sundered lines of the True Men and what was to be left of Elvish blood in Middle Earth after the great Departure that ends Tolkien's book, well, THAT'S the STORY. That romance. The rest of the things are there to make it exciting, like the Civil War in "Gone With the Wind" or the Russian Revolution in "Dr. Zhivago" or the sinking of the ship in "Titanic."

For Tolkien, on the other hand, Aragorn, future king though he was, was very much a supporting character. His story is about hobbits, small, frightened insignificant people, who came to be counted among the Heroes of the Age, and in particular Frodo and Sam (and, in his own twisted way, Gollum, who is also revealed to be of hobbit-kind), on whom in the end the entire Fate of the World rests. It is Frodo's burden to take the Ring to the Fire. The others are only appointed as companions for him.

The story of Arwen and Aragorn is perfect exactly where it is, available in an appendix for those who are interested in it, necessarily hinted at through bits and pieces of it that intersect with the Tale of the Ring, but not intrusively thrust into our consciousness, distracting us from the Main Story. One might wish it were told at greater length, in more detail, but I don't find its placement in the appendix to be in any way a storytelling failure.

I'm not quite so sure about Hitler's conception in "From Hell." I like the footnotes, and in the main enjoy the interaction between the narrative and the notes, but that one may have been going a bit far, reaching too much toward something that just didn't really belong (he admits reaching on the dates to fit it in) and which literally makes no sense at all without the footnotes. That may, in fact, be a storytelling failue on Moore's part. But I still like it.

Just on an aside, I found something interesting:

Grant Morrison's first DOOM PATROL issue was #19, and his last was #63.

And Alan Moore (and Rick Veitch, Steve Bisette, John Totleban, and many others) did a mini called 1963.