That was my initial reaction to that statement as well, but upon reading on I realized that's not the point they're trying to make. They're not saying "respect our efforts," they're saying "we spent a year on designing this to be challenging and replayable," and they go on to provide evidence for their claims of superiority.
It's actually a big compliment, too. It signifies the design is conceptually sound and as small as it could be.
The thing with 2048 is a bit different though. It wasn't just a game craze, it was people playing with algorithms. Making a funny/curious clone of the game had become the game for some.
This is the critical point missed by calling 2048 a clone. Of course it's a clone, and that's what makes it so interesting.
2048, in isolation, isn't that much fun; it captured interest for a while, but what made it gain popularity was being so simple that it lent itself to a hundred variations. Every one of those is, in some ways, more a "clone" of 2048 than 2048 is of Threes, but the meta-game has become fun in ways the game itself isn't. Just look at things like Flappy 2048, or Numberwang 2048.
I don't think we can know why 2048 became so popular and Threes fell in its own shadow. Maybe it's a sign that open source and free as in freedom have finally registered with the general consumer on an emotional level, though I doubt it. If we knew for sure then we could make such better toys that the kids ignore the box.
I think this is an important reason not to dismiss the Web as a platform.
See how easy it is to shoot down someone's opinion and state your own?
Then again, it might have seemed even more bitter if it came after all the discussion of their work.