The eshop is a bit different than before, so it might be possible.
But I thought Team Meat will only port TBOI to 3DS?
Team Meat didn't make TBOI. Edmund drew the art, but Florian Himsl did most of the programming.
Both of them have submitted a 3DS port to Nintendo, but Edmund hasn't recieved word yet if it's going to be published.
SMB isn't going anywhere anytime soon. However, I did hear of a remake
of SMB for Apple Devices. You could ask Edmund on that. Who knows? Maybe it will even have a level portal that actually saves progress?