It's a well-thought out move by Nintendo and Game Freak. The DS, like all systems before it, has run it's course. And to do a game of this magnitude on a lower-level game system would hinder it completely, even demolish the whole game's upgraded value. The DS has been around for awhile now, and the 3DS has been having record sale. With Pokemon as a guide, those who don't have a 3DS will get one, it's inevitable. While I still love my old DS Lite, my 3DS needs a little more love, since I only really use it for trading and as a back-up when the DS Lite's battery is charging. I may just have to buy another one so I can continue trading among myself. But it's time the games moved onto a more powerful console that can handle the updated graphics and whatnot.
People will be willing to pay the price for a 3DS if it means they can have a powerful, awesomely designed, and highly popular game on it. Hey, I was willing to pay for a PS3 so I could play Ratchet and Clank Future series and beyond, even though for a long time I wasn't willing to do so. It's a smart move, and the 3DS needs something highly popular to motivate it's sales and make it seem more desirable. I don't follow your argument much at all. Technology evolves and upgrades as time goes on, while older versions goes obsolete at the same time, so it's only natural they would use a more powerful system for a newly upgraded, yet highly popular, game series. It only makes sense. So, no, it is a very intelligent maneuver on Nintendo and Game Freak's part. Plus it will just create more profit for Nintendo in the long-run.