I don't know what kind of 3DS friends you have or what kind of 3DS games you're playing, but I have found myself in very few circumstances where I've wished to immediately send a message to someone in the five seconds between Mario Kart races. Nintendo is not and has never been about "feature parity."
Sending messages of this sort to people for them to check at their own convenience sacrifices the fringe needs of the minority (immediate, pervasive instant messages) for the perks of the many (character-filled personal drawings and messages to be checked and looked forward to at the user's own convenience).
Think about it as the difference between sending a text message and sending a letter: text messages (or instant messages) convey information, but something like a letter is something to be anticipated and created. It's more fun and more personal, it's more compelling, and it's something people can actually sit down and "use" as entertainment instead of just utility. Anyone who expects anything different from Nintendo clearly doesn't quite get it yet.