Small changes that mean a lot to me: In the eShop, when you buy something from your Wish List there are a number of improvements. First, your entire Wish List is displayed at one time instead of being broken into multiple pages. Second, you have the option to download a purchased title right away or to wait and download later (in the background). Finally, you now return to your Wish List after buying something instead of being kicked back to the main screen.
[Edit: The abilities to add only the required funds for a purchase and save password-protected credit card information directly on the system are also great.]
I know the update didn't do anything amazing... but it has added some neat functionality and made using my 3DS even easier and more enjoyable. Nice.