They're pretty much giving Pokemon away since most people buy games like SM3DL and MK7 when they buy a 3DS anyway. Why wouldn't they make the games you need to register games that don't already sell a bunch like Kid Icarus or Fire Emblem?
They're obviously trying to move 3DS units, and making people buy Kid Icarus or Fire Emblem, as you yourself described, is a much harder sell... than telling people if they buy
Mario Kart or
Mario Platformer(3DL) they get a legit
Pokemon game for FREE with their 3DS purchase! I think its a great marketing move.
Imagine if it was 3DS + Pokemon X/Y = free MK7 or SM3DL (or other--including KI or FE). Those franchises would unfortunately be the afterthought... but since it isn't... potential buyers are now choosing a specific franchise,
helping recognition, to
GET a renowned
Pokemon game. (I think maybe some people are forgetting how big Pokemon as a franchise truly is)
I also think that the way this is setup, Pokemon, Nintendo's guaranteed draw, won't be available right away... leaving customers only to play the games they purchased, at least initially... until the deal is honored. Ultimately, I believe this will definitely help exposure for their other 'more' popular IPs (Mario/DK/Animal Crossing)