Mother 3 had a lot of hurdles Xenoblade at the least doesn't have:
1. Mother 3 was never translated by Nintendo into English in any part of the world, there's only a fan translation.
2. The game was coded in a way that made translating very difficult, which would further disincline Nintendo from wanting to bother.
3. The game came out almost two years after the DS debuted, and the last game worth giving a damn about was Final Fantasy VI Advance, hitting in January and thus less than a year after Mother 3's debut.
4. There MIGHT be some of the same legal issues plaguing it that plagued Mother 1 + 2, which have yet to hit the Virtual Console in any part of the world.
At least 2 of those don't apply to Xenoblade (there could always be legal issues for the US but not Europe/Japan, or at least cultural issues), and it seems to me like the game's probably coded in a translation friendly method if NoE's translating it, and that won't even matter unless NoA decides they MUST translate from scratch.