Doubt it.
Nintendo's current sales of the 3DS have not been too hot this year, so they can take what they can get. New 3DS will probably be on the same level as the DSi, and have a small attach rate at launch from hardcore supporters and people coming late will pick one up.
Thing is, releasing a New 3DS version only would alienate everyone who has a 3DS/XL/2DS, and that would be pretty fucking bad. That was one of the core reasons Gen 5 was on DS, because the attach rate of the 3DS was not quite there yet + they needed something out that year.
At most, we will probably see some special features for the New 3DS version, and that be about it. Thats not to say they won't pull it with another franchise (I totally see them pulling it with a Majora's Mask 3DS version), but not Pokemon
