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.
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.
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.