Threes vs. the clones
Probably most independent game developers have read by now the long post about cloning of their game, from the creators of the Threes. If not, I encourage you to read it now. I personally learnt about 2048 before Threes. Somebody showed it to me, proudly pointing out that it was made by a friend of him. He seemed unaware that his friend had cloned another game, and it would not surprise me if 2048 developer had no ill intentions at all (and the developers of Threes seem to hold nothing against him).
The problem with puzzle games
I think a big problem for puzzle games is that the idea behind them is usually easy to copy. Just take a look at all the match-three or tile matching games out there. The basic idea is usually so… well, basic, that it is not the main obstacle to make a clone. This does not mean that it is easy to come by or to make it work right (just look at all the work it took the creators of Threes), but that after seeing it, you can understand it immediately. Which is actually something sought after, because these games tend to be abstract, and you need the players to understand them easily.
Can they be made harder to clone?
Sometimes mechanics include subtleties that are not easy to get right, like difficulty balancing or usability. When playing Bejeweled, you will never run out of possible moves, for example. That might not be so difficult to copy, but I’m sure the exact algorithm they use for deciding which jewels will appear next has a lot to do with the feeling of flow the player gets, and is not so easy to make right. Good usability is definitely not easy to come by, and bad usability means that players will feel frustrated very fast. I have not played Threes so I cannot talk about it, but I do not like that 2048 seems a bit too random. Just popping numbers here or there does not cut it. I have not looked at the source code so I might be wrong, but the point is that for making a game lasting and enjoyable, these details matter a lot.
This gameplay balancing may only have to do with visible things, like which actions are available to the player, or what elements compose the puzzle. And if it is plainly visible, it is easier to copy.
In a game like Flip, the basic idea (flipping the groups of pieces) is certainly simple, but two things would make a cloners’ life difficult: usability and levels.
Flips basic gameplay is easy to clone, I actually implemented it in just a couple hours using right mouse button clicks to flip right, and left button to flip left. Of course that would not work on a touch device, so I decided against it very early in the development and switched to grabbing and moving the pieces. And making the actual grab manipulation feel right took me a long time, lots of testing with players, and a lot of experimentation. Cloning that feel would not be easy.
And regarding levels, because of the nature of the game itself, it is impossible to clone it without just copying the levels. To know for sure the minimum amount of moves for any puzzle except the most trivial ones, you need to program a level generator/solver (to provide hints, you also need an efficient way to store the information generated in a way that fits in a tablet and is fast to use). If you don’t have experience doing puzzle generators or solvers, or some computer science background, know some graph theory and/or search algorithms, you will have a hard time at it. And if you are able to reproduce it… you will just end up with the same levels! From what I’ve seen, most people who clone do not dedicate a lot of time to it, and will probably be set aback just by the task of making a proper level generator.
Of course, it is also possible to alter the game mechanic, adding more elements to it or more actions for the player (like swapping some pieces in the middle). But then you need a more complex level generator. Good luck again with that.
So what then?
In the end, cloning is not a problem that only puzzle games have, but the genres intrinsic characteristics (simple mechanics, easy to understand, mostly everything should be visible to the player, not a lot of content production) makes them a perfect target for that, and developers should be aware that value should be put in other areas to make it stand out. And I guess that has worked in the case of Threes, as they seem to have made good commercially with it. Dealing with the emotional/personal side of cloning is, of course, another matter.