I don't find it "suspicious" at all. I'm sure it was completely intentional. Nintendo most likely didn't want the romhack to impact sales. And it does impact sales. I'm playing Reborn, but I haven't bought a Pokemon game since Platinum (that was the only game I ever bought). I actually feel kinda bad about that...
While I agree that I would be great if Fan Games could exist, I don't fault Nintendo for reigning them in some. Whether we like it or not, it does affect the way their franchise is viewed, sometimes positively, and probably affects sales.