It's fair to say 2048 is a shameless rip-off, but that doesn't mean it's not better in ways that matter.
In 2048 you can keep playing far longer and are much more in control. Sometimes you get a number in a bad spot, but some strategy and additional luck can get you out of many of them. The sliding mechanism is also behaves differently which significantly changes the gameplay.
Mario "stole" from Snokie which "stole" from Quest for Tires which "stole" from Jump Bug which "stole" from Wanted: Monty Mole which "stole" from Donkey Kong which "stole" from Space Panic.
The entire history of video games is taking an existing concept and adding small tweaks to create something new. Threes/2048 is no different but for some reason and incredible amount of emotion and vitriol is tied up in this one.
I had played 2048 first so when I tried Threes, it didn't feel right to me at all. If I had tried Threes first, I probably would have had the opposite opinion.
Some of the rules are slightly different (I don't remember how), but the two games are pretty similar. Other than rule differences, the sounds in Threes were very grating to me. I ended up muting all of the sound effects and music. One huge plus to 2048 (IMHO) is that it was released as open source.
It's like comparing Chess and Checkers. Similar sure 8x8, move one piece at a time, promote on other side of board etc, but they play as very different games.
This is nothing against this article, of course, which is an excellent write-up. But: if you like 2048, you'll like Threes better, and the creators of Threes deserves to be rewarded for coming up with the design.