I'm not sure. It's true that there are a lot of similarities between the two, and that Squadron Supreme came out first.

It's because for all their surface similarities Squadron Supreme was a typical Marvel comic of the mid-to-late'80s in look and feel while Watchman was a groundbreaking, breathtaking exploration of narrative techniques rarely seen before in the medium. It's kinda like the difference between a better-than-average episode of Gunsmoke and Clint Eastwood's Unforgiven.

Cei-U!
Tain't the story ye yell, tis how ye tells it!

Without trying to be flippant, it's the same reason more people talk about Michaelangelo's work in the Sistine Chapel than they do about the works of Cristoforo da Bologna. Both artists dealt with Biblical subjects, but there was a massive difference in depth, innovation and execution.

Squadron Supreme was a story with an interesting premise, I'll give it that. Superheroes getting down to Earth to try and resolve problems that affect real people, and finding out that you can't solve things like world hunger or urban violence just by punching people. That's cool. But the storytelling was quite formulaic, the characters were pretty two-dimensional, the artwork was barely average. There was no second-level reading to be made of the series; it was just an O.K. superhero story that tried a somewhat new twist.

Honestly I don't see that much resemblance between Squadron Suprme and Watchmen. As most of the former dealt with heroes fighting one another over what the government should and shouldn't do, I'd say that Civil War was more like SS than Watchmen might have been. Yes, both SS and Watchmen asked the question "how far can someone in power go in the pursuit of the common good"; but that's a theme we had already seen before, as in Star Trek's"the city on the edge of forever", in the German SF series Perry Rhodan or in Jim Starlin's Metamorphosis Odyssey.

Two words...Dave Gibbons. Bob Hall and John Beatty delivered a typical if pedestrian house style looking comic book. Gibbons provided a tour de force visual masterpiece using the 9 panel grid for the most part and broke new ground in the ways a comic book story could be told visually. The structure of the 9 panel grid made what would be an otherwise very dense story accessible to all audiences, not just though who were already comic literate. There is never a question where the eye should go next in Gibbons' layouts or page structures, yet there is a lot of visual interest throughout the book to please the eye as well. The characters are visually distinctive both in costume and out, which also goes a long way to making the book pleasing to non-traditional comic readers. They're not scratching their head wondering if that is Peter Parker or Piotr Rasputin when in civvies like they would with a lot of typical comic book art, which is the kind of art Bob Hall and company delivered. Gibbons lettering also played a large role as did John Higgins coloring in making this a visually accessible and pleasing package.

A lot of what Moore did in the book has been blunted by those coming to it after the fact used to seeing the things he innovated used (but more often misused and abused) by those who followed, so the groundbreaking effect of it is lost on some, but what Gibbons did with the visuals has stood the test of time (that's not a knock on Moore, he had no control over what people did afterwards but it does add to the noise of those claiming Watchmen is "overrated" but despite that what Gibbons did is still there). Squadron Supreme never rose about a typical comic book story visually, and was never accessible to an audience not already steeped in comics literacy. If you stripped all the text out and mixed up the pages of Squadron Supreme with a bunch of other pages from Marvel comics of the time, it would be hard put for a casual reader to pick out which ones were Squadron Supreme. Watchmen pages would stand out from other DC pages of its time and be easily recognized. Comics are a visual medium and art that invites audiences in and makes it accessible and enjoyable potentially to any reader, not just a comics fan, is going to go a long way to fueling the regard the book garners and the respect it gets in the long run.

-M

That's because of a couple of things:  it's barely been seen, let alone read, by most; and, Veitch's art was very steeped in the Underground style, which put off a lot of people.  It's narrative is also of the Underground style and it takes some time to sort things out.  Moore pulls you in, well, more, from the get go.  

The One was an Epic mini, which means Marvel didn't promote it.  The only ones they put any muscle behind had the Frank Miller name on them.  Archie Goodwin oversaw some great material; but, he was about the only one at Marvel who cared about the Epic books, after the initial launch of Epic Illustrated.  When it proved no challenge to Heavy Metal (in  sales, not quality), the rest of the company seem to take it as gospel that they knew better.

In terms of story, Veitch's Brat Pack was more accessible (though just as repellant, if not more), while the One was a bit more along the lines of Maximortal.  The whole King Hell Heroica is a very acquired taste, for most.