I don't really understand it either, it seems kind of a random thing to do this for the 3ds which is already their successful console, I guess they are just trying to double down on leveraging the 3ds, but now they risk alienating a lot of players who already have a 3ds, etc.
However, for someone who doesn't yet have a 3ds or a Wii/Wii U (and hasn't played Xenoblade, perhaps not a large group though), it sounds like it could be a good deal.
I'm also glad that Xenoblade has been getting some big recognition, it's been an exciting series all the way back to Xenogears and through Xenosaga and it seems like a lot of people are finally seeing that one way or another.