Reggie's wording is real odd, but the intention seems pretty clear: AM2R and fan games like it (that is, games which emulate a commercial product) pose a drect threat not only to Nintendo's sale of those commercial products, but their retaining of the IP as well.
Like others have said, it's not some sort of weird conspiracy of Nintendo getting scared or whatever because of some fan game. That's a pretty ludicrous idea, and if you truly believe that, you're letting your anger over AM2R's C&D get to your head.
Not only is Nintendo selling Metroid II on the VC, they're also working on a remake of their own, and this fan game threatens the sales of both by being free. Sure, Nintendo didn't C&D the game until it was finished, but that's very likely due to Nintendo themselves not knowing of the project until it was finished, since the finished product did get a lot of enthusiast publicity after release.
Nintendo's been pretty lenient with ROM hacks and the like in the past. Maybe not as much as SEGA, but no one else in the industry really is. But Nintendo has made the line pretty clear recently, and that line is with fan recreations of available products. Nintendo also shut down games like Zelda Maker and the Mario 64 Unity remake, and those barely got off the ground prior to getting taken down. So AM2R being taken down makes perfect sense, as disappointing as it is.