This is certainly true enough, with Mass Effect 3 didn't they have to release a patch that redid the ending or something? And the fan translation, while not perfect (right now it's riddled with typos) is pretty comprehensive.
If Nintendo learns its lesson, I wonder if they'll just hire the fan translators rather than dealing with Treehouse for the next installment. That's not entirely unheard of--there's a recent visual novel game on Kickstarter, Muv-Luv, where some weebs made an unofficial translation of it. Later on the Japanese creators just emailed them and asked them to work on the official release, which they happily did. Now pretty much the only thing the Japanese creators had to do was give the original fan-translation some light editing and double-checking, improve the VA (the original had terrible, terrible Engrish), and send it out. It certainly seems more economical than this localization chaos.