The "fanboyism" around these two games is crazy. 2048 might have been a knockoff, but it's a very different and unique game. I actually really dislike Threes because it's a "play until you get screwed by the RNG" type game. I gave up on Threes after about an hour (I didn't "refuse to even pay a little") and went back to 2048.
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.