They said they were based on 1024, and 1024 explicitly launched with an app store description along the lines of "Why waste your money on Threes, we're free".
EDIT: Found the quote. Surprise surprise it's no longer in their description.
"No need to pay for ThreesGames. This is a simple and fun gift for you, and it’s free."
He was cloning 1024 which was explicitly a clone of Threes. I was only pointing out there was a chain there.
The innovation appears to have advanced enough that some of the 2048 variations are more akin "Doom clones" and "Roguelikes" than they are to "app store clones". But the 2048 apps that have flooded the app store and are mostly direct clones of the web 2048 versions. And they exist in a previously unnamed space between "clone" and "variation".
Search for a game. The set of games is displayed with an install link and a screenshot. The description needs some scrolling.
(Edit: bizarrely heavy downvoting in this thread)
The webpage for that 2048 references Threes, so even he is supporting a line of direct influence.
One of the clones was amde without being aware of Threes!, other people are using the term "rip off", not me.