Nintendo, up to this point, has forced Wii U and 3DS owners to keep their respective eShop account balances seperate. As you might understand, this is a setup that works largely in Nintendo's favor and has little benefit for consumers. Luckily, apparently Nintendo has received enough criticism over this and will be changing it starting in December. That's right, soon Wii U and 3DS owners can combine their eShop account balances.
Overall, the change isn't hugely significant. There's still no system in place for Nintendo users to have an overarching account with extensive features or the like, but simply having the option of spending a balance on either of Nintendo's systems is landmark for Nintendo. Remember, these are the guys who still have friend codes implemented on all their platforms. They're about 10 years behind everyone when it comes to online services.
That's not all that will be coming in the 3DS system update, however. In addition to the account combining, the 3DS will also be acquiring its very own Miiverse. Yeah that sort of odd Wii U feature that lets players post images, tips or insight into various "communities" is coming to Wii U.
Check out the Nintendo 3DS update starting in December, I suppose. Who knows what else might be included in the thing. They're never exactly what they appear to be. Oh, should also mention that if you have different IDs on each device then you won't be able to combine your accounts. Nintendo.