I've been meaning to make this pont for awhile, now seems as good a time as any.
Nintendo works like most other multi-nationals, in that each "division" is a separate company. What I think this means on a practical level is that, though NoA and NoE take direction from "head office" in Japan, they each have their own business targets for the year and, more importantly, their own budgets and financial accountings. Bear with me here, I'm going somewher with this.
During the past fiscal year, which ends shortly at the end of March, NoE spent some of its operating budget on localizing and releasing the Op. Rainfall games. NoE has to pay for that activity out of its own budget and account financially for whether or not that business direction was ultimately profitable. It is its own little (or not so little) company. Its financials roll up into the parent company's financials, but NoE also wants to be profitable independently, on its own balance sheets. Same with NoA.
So NoE expends funds and effort and comes out with 3 localizations. Those are NoE's assets. I'd be willing to bet that NoE would not (could not, by accounting rules) just hand over those assets to NoA free of charge. NoA has to pay for those assets (localizations) and probably at "fair market value". So Reggie et al. have to use their budget to obtain the localized versions of the games and, as others have pointed out, spend NoA money to press the discs, advertise, distribute, etc.
NoA assesses the likely North American market and decides the games have a risk of being not profitable, or maybe only marginally profitable. So, it shares the risk by cutting deals with Gamestop and XSEED. Probably a sound business decision and one based on expenditures solely from NoA's budget. Not NoE's nor head office.
This consideration of what NoA has to do to release the games has been missing from every commentary I have seen. Almost all criticism of NoA's decisions includes something along the lines of "NoE has already done the work, why doesn't NoA just release the damn games? NoA doesn't have to pay for the localisation." Well, I am pretty sure they do. And they make autonomous decisions about their market and their bottom line.
I also think NoA was particularly concerned to do two other things:
1. give Skyward Sword breathing room in the market; and
2. stretch out the few remaining Wii releases available throughout calendar year 2012.