Making 1024 and putting something akin to 'Why waste money on Threes, here's a copy' in the app description was just classless though. I don't see any redeeming value in that.
Additionally, from the article: "For the makers of “Threes,” the good news is that the emergence of the clones hasn’t decimated its market share – the app is still a Top 10 title in Puzzle Games, Card Games and the general Games category in the U.S. and a top 20 Overall app on the U.S. App Store. (All Paid rankings, which, to be fair, is less competitive than the Free ranks.)"
It's also important to note that just because I played doge2048 for a few hours doesn't mean that I would have been willing to pay $2 for Threes. 2048 and it's variations exposed me to his idea, but did not cost him my purchase.
When you choose to do closed source software that's the trade-off you're making.
Also, most of this has been on github, which has nothing to do with app stores anyway.
This is still a big problem Apple has though. I have a hard time with the whole "curated app store" thing when nearly every search turns up screen after screen of low quality copy-cat garbage. How long was Pokemon Yellow on the store before it finally got pulled? How many 'strategy guides' and 'Angry Falcons' and 'Crash of Clans' are there?