The DSi and 3DS have that specific SD Card slot cover so that the SD card doesn't accidentally eject in your pocket. It's a little tougher to open than the door on the Wii or Wii U. There's no need for one of those on a home console. If Nintendo does redesign the console, I'd expect the cover for the sync button and SD Card slot to feature the same out-of-the-way, sliding in-console design as the Wii U.
I don't know if Nintendo would switch back to a top loading design because the Wii has that ridiculous LED around the disc slot that tells when you've received WiiConnect24 things. I guess they could just put the light somewhere or preferably, make it less intrusive. If it was top loading, I'd expect it to pop up like the GameCube instead of that ridiculous sliding door that the new PS3 has. Why would Nintendo copy the worst design choice on the new PS3 of all things? And besides, with a design so small, the door would be hanging over the console itself making it flimsier and more prone to getting caught on things. Again, I'll take that bet if you really believe it.