If 2048 is killing Three's revenue stream (massive assumption there in your article) then its not the result df indiscriminate cannibalisation of an idea, but testament to the better marketing that 2048 has engaged in (whether intentional or not).
The makers of Threes made a great game, because they love making games, and i suspect that their motivation for work, is about making great games, not revenue. I make this point to question the true effects (if at all) this 'revenue stream killing' effect will have on the makers of Threes.
Surely the lesson is, if you're an indie, make great games. Then pay great marketers to let people know about your game. Maybe all game releases will have accompanying marketing strategies, where the main paid for game, will be partnered by a clandestine release of a 'rip-off' app to boost exposure in the blogosphere.