In regards to the ending of Watchmen, I think the comic ending makes more sense in-universe (as has already been noted, an alien attack is probably more likely to unite everyone than an attack by an American superhuman) while the movie ending makes more narrative sense, since the comic ending – despite some foreshadowing – comes very unexpected and goes against some assumptions in the story (like Dr Manhattan being the only one with actual super powers. Which I don't know is ever actually stated, but it's definitely the impression I got as a reader).