Well, to you, is it worth being stuck with Japanese language in the firmware and having to download every update/DLC as a CIA file rather than being able to just get it from the US eShop?
Only you can answer that question. But to me, it doesn't seem worth it.
Plus you'll need Cubic Ninja or OoT to use the GW and Japanese versions of those are more expensive AFAIK, not to mention harder to get unless you live in Japan.
You can always perform a region swap of your emunand, making the japanese bit irrelevant. Haven't done it myself, but I believe there are
tutorials in the
tutorial section on how to do this. I'd say get the Japanese one at that price difference.
eShop won't work after the region change.
There's a workaround for that, but I heard the workaround only works on consoles that didn't come with a preinstalled game/software, and every n3DS comes with a preinstalled title, for EU it's a special Tomodachi Life demo.
It's also a pretty complicated and risky process, and it requires a unique donor NAND unless you want to risk getting banned by using a public SecureInfo file.
I wouldn't recommend it.