This is the message I see every single time I open my gates or go to visit someone in my Japanese copy of New Leaf (tobidase). It's saying we both need Version 1.1, which you got by using the update option from the start screen after hitting the "A" button. Western versions of this game came with this update installed already (sounds like Welcome Amiibo), so they don't see this message. It's a bit annoying, but I've learned to deal with it. What's more, the update is saved on an SD card, so if a cartridge version is played without that card, it'll revert back to version 1.0, and you'll lose the ability to travel until you put an SD card with the update data in the system. I'm not 100% sure, but I would imagine if you don't connect New Leaf to the internet, you shouldn't have a problem playing without the update, you're just limited to playing it like you can now, so in that way, I'll "test the waters" with my used NA copy of New Leaf before I update any of my other copies.
