An account system is coming to the Nintendo 3DS in December, Nintendo announced during a Nintendo Direct presentation this morning.
Update 2: More details regarding Miiverse here. Nintendo Network ID details here.
The update will allow you to use the same Nintendo Network ID across both your Nintendo 3DS and Wii U consoles, and share Nintendo eShop credit between the two systems this way. Alternatively, you’ll also be able to create a new Nintendo Network ID for your 3DS, but this will mean being unable to combine your eShop credit.
Nintendo have not yet announced if the introduction of the Nintendo Network ID system to the 3DS will allow you to link games to your account rather than your 3DS console.
Additionally, Miiverse will be coming to Nintendo 3DS in December as well, alongside the update that adds the account system to the console.
Stay tuned for more details.
Update: Added clarification regarding game purchases being tied to account as opposed to hardware.