Remember. As random people added other people random Friend Code, some started trolling as they sent NSFW pictures on swapnote to the point users reported said content and Nintendo decided to make it Streetpass only because of said issue. I would like your idea of a messaging system in nintento 3ds or wii U but, with the way people are, I doubt it will happen.
I wish there was an easy way to message friends on the 3DS and Wii U asking if they wanted to play a game or whatever. As for whether they'll implement it, possibly on the NX? I still know nothing about the console, but if they want to be on par with the Xbox One and PS4 they'll need to step up their game and add some new features. I doubt we'll see a message system added on the 3DS though.
It was actually pedophiles using Swapnote/Letter Box to get nude pictures from underage girls. Nintendo learned of it and shut down the SpotPass functionality, as it wasn't possible for them to moderate the messages, and leaving SpotPass functionality in would've put them in an embarrassing position.
Miiverse isn't a perfect replacement, but I think that on the 3DS it's all we're getting. I just hope they find a good middle ground, one where friends can talk to each other directly in an environment that can't be abused by those kinds of creeps.
I'm still mad they neutered Swapnote because pedophiles got a hold of it and ruined it. The StreetPass function is ultimately useless as well unless you're friends with whoever you're passing because until I added some classmates back when it was still functioning, they weren't getting my Swapnote StreetPass and I wasn't getting theirs!
I'd love a messaging system on the 3DS/Wii U/NX akin to the PSN honestly. Someone's sending harassing messages? Reported and blocked.