I could not tell you why they wouldn't go to the trivial effort of including a mirroring function. Maybe it wasn't trivial.
More than any other trait, physical or mental, cultural or philosophical, artistic or scientific, left-handedness is the trait I most strongly identify with. You show me a left-handed character in a story, and I'll drool. Link has always been left-handed, until Twilight Princess for the Wii came along and test players started reporting that, being right-handed, they couldn't handle a left-handed Link. So Nintendo mirrored the entire Wii version of the game. (That version has also been struck from series canon, as far as I'm concerned.) And now with Skyward Sword there won't be any left-handed version at all.
Link is just about Nintendo's only prominent left-handed game icon. You could make a non-watertight argument for Samus Aran, and they occasionally show up as less-iconic characters (like Crono and Frog!), but, really, Link is pretty much the only top star.
I know most people don't really care, beyond the left-handers who complain about once again being made to play right-handed, which is a poorly addressed problem in the industry. But I care for narrative reasons. I like to identify with people in stories--I think we all do--and, whether or not it makes sense to others, I really identify with left-handedness. It aggrieves me that Nintendo would turn a left-handed character, and essentially its only left-handed star, at that, into a right-handed character without any consideration given of the narrative impact or the practical one.
It really bums me out.