You also have to remember that Science Fiction as a classification simply did not exist until the late 30's. Until then books were pretty much either Fiction or Horror
Close, but not quite accurate. The usual date is 1926, with the publication of Gernsback's
Amazing Stories; though Munsey magazines and the like, around the 1890s to the 1920s, published a great many stories (and writers) considered classics (and founders) of the field, such as Burrough's early John Carter stories, George Allan England's Darkness and Dawn trilogy, stories by Garrett P. Serviss, etc. The late 30's is actually the date of the so-called "Campbell Revolution" or "Golden Age", under the aegis of the late John W. Campbell as editor of
Astounding (later
Analog) -- as well as its sadly short-lived fantasy counterpart,
Unknown (later
Unknown Worlds).
However, your point about
The House on the Borderland is right on the money, as it was long considered a classic of the field. And, like so many things of the time, it straddled what would later become more rigid genres -- in this case, the weird tale, fantasy, and science fiction, much as his
The Night Land also did. The same is true for many of those who were long viewed as major writers in the field from the period, such as A. Merritt, much of whose work does blend sf and fantasy by blurring the lines between the two -- something which remained quite acceptable in sf for a very, very long time; certainly throughout the Golden Age itself (see Kuttner and Moore's "The Children's Hour", "Mimsey Were the Borogoves", and "Vintage Season", for example).
As far as the opening question... I don't know as Wells is/was the greatest sf writer... I don't think a field as broad as sf (or any other) can produce a single "greatest" writer... but he is certainly one of the most influential and important.
Oh, and as for alien invasions... try Fitz-James O'Brien's "What Was It?" or Guy de Maupassant's "The Horla", or even Ambrose Bierce's "The Damned Thing", which gives a (more or less) scientific explanation of the invisible invader....
Time travel? Asimov included "A Christmas Carol" in that camp, and that certainly predates Wells by a good many years. And, if you'll look at this Wiki entry, you'll see that time travel (granted, not using technology... but then, Wells' Time Machine is scarcely a well-developed scientific -- or pseudoscientific -- concept) as a theme dates back at least as far as the 18th century:
List of time travel science fiction - Wikipedia, the free encyclopedia
It isn't so much that everything is a new telling of an old story; closer to the mark is that basic underlying
themes are used and re-used, though in vastly different ways and often presenting vastly different stories (with correspondingly vastly different moods and impressions).
And for anyone interested in a broader view of the sf of the period 1890-1920, look for some of Sam Moskowitz' anthologies, such as
Science Fiction by Gaslight or
Under the Moons of Mars: A History and Anthology of the "Scientific Romance" in the Munsey Magazines, 1912-1920, or, for a broader period, Damon Knight's
A Century of Science Fiction....