Also, remember that Starling built the EMH's holo-emitter, which continued to exist even after "Future's End" was over.
Also, when the Voyager crew visit LA in '96, they don't seem surprised by anything around them and act as though it's normal.
The USA was involved in multiple wars in the 20th century, but not one of them touched American soil, aside from a single Japanese fire balloon belatedly killing a Sunday-school teacher and five children who found it in the woods. And WWII was the largest-scale war in history. So a war doesn't have to destroy American cities in order to have American involvement.
As I said, that was probably an alternate past anyway. But I think it likely that the US avoided being directly affected by the Eugenics Wars, which seemed to be mostly waged elsewhere in the world. If the Khan comic implies otherwise, I'd consider that an error, or at least something that would need to be justified.
To be fair, we actually saw very little of the US in that episode. A few parts of L.A. and that was it.
Interestingly, Star Trek: Federation states that North, Central and South America were unified into the American Empire at the onset of the Eugenics Wars.
No, actually, it doesn't. Nowhere in that book is the phrase "American Empire" ever used. The book does make heavy use of the term 'Optimum Movement'. Is this what you were referring to? (And, IIRC, the Optimum was not an American grouping. Optimum took over many countries worldwide, not simply the US.)
Spoiler: Part Two Moscow and Washington nuked on September 17, 1992. I would've been five months old. The Augments essentially annihilate the world's military, the zeppelins we see in London are shown here. Personally, I hope they flesh out the Eugenics Wars more, the Augments seem way too powerful. Khan heads back to India and defeats the Indian military by his lonesome and begins calling himself Khan. The world is split up 7 ways. It's really, really dark and conspiracy theory-ish. Pretty cool for Trek.
What, and we're supposed to believe that despite these MASSIVE cataclysmic events, after the Wars were over, things just went back to normal, with the rest of history up to the present happening more or less as normal? 9/11 and the War on Terror still happened? The Beastie Boys still happened? No way!
Well, in the first place, no version of Star Trek is the future of "our timeline". I have never assumed that the past of Star Trek was my present (even as the six year old I was when I first started watching it). As someone else pointed out recently in some thread around here, different laws of physics, a different kind understanding of biology, historical events that have never happened--these are all parts of Star Trek's past that require it to be in an alternate universe anyway, from the get go. As such, any deviation from our own "timeline" is perfectly acceptable, in principle. As to the specific story in the comics, remember who is telling the story. To what degree are we to simply accept everything Khan says at the trial depicted in the story?
Records of that era do still exist in the 23rd century, so his prosecutors would be able to find out if he was telling the truth or not. You couldn't just obliterate an entire major city and have no one know about it generations later.
But it's more a matter of what Trek itself has established about its own history. The later shows have established that the late '90s and early '00s went pretty much the same way there that they did here; for instance, in ENT: "Storm Front, Part II" we saw footage of the 9/11 attack as history was resetting itself.
Doesn't making Trek entirely an "alternate timeline" thing kind of detract from the point of the show which was to show humanity's potential? If it isn't OUR future, that kind of makes the whole thing feel a bit hollow.
Why? So many things that were presented in "our time" have come and gone without actually happening. That ship sailed a long time ago. This may only (quite likely) apply to me, but I treat Trek the way I treat Bond. If multiple instalments seem to fit together, then they fit together. If they contradict a previous or future instalment in a significant fashion, then it's just a different creative take on the character/universe. Solves a lot of problems and makes enjoying the various iterations far less stressful. YMMV