It was confirmed recently by Satoru Iwata, when revealing the New Nintendo 3DS models, that a port of Wii title Xenoblade Chronicles will be exclusive to the new hardware to utilise its improved CPU. It was unclear how common this would be, yet in today's surprise announcement of the hardware hitting Australia and New Zealand on 21st November, Nintendo Australia Managing Director Tom Enoki used the plural 'games' when referring to exclusives for the hardware, though only mentioned Xenoblade Chronicles for a 2015 release.
More interestingly, and dispelling any doubt that translations of the previous Japanese broadcast can raise, Enoki has made clear that multiple projects are in development that will offer improved experiences on the New systems — this suggests that they'll be available across the whole 3DS 'family', but will be preferable on the latest hardware.
You can of course play all previously release Nintendo 3DS titles on New Nintendo 3DS; the gameplay and graphics for these titles will not change by playing them on the new consoles. But we have already started developing new titles where gameplay can be improved and graphics enhanced only from playing on New Nintendo 3DS.
We already know that Super Smash Bros. For Nintendo 3DS will only allow direct access to Miiverse on the New models, being unable to do so on the existing hardware. These comments from the latest Nintendo Direct will raise concerns of splitting and fracturing the 3DS userbase, however, especially if there are a significant number of these games that offer differing experiences across the systems; it could be divisive. Much will depend on the nature of the differences and number of games, but this could be a risky move by Nintendo in alienating some existing customers.
Let us know what you think of this in the comments below. If you want to see the sequence in question, watch the video below from the 5 minute and 30 seconds mark.