Hopefully when Nintendo releases their next portable and console they use the same format. Own both systems and you're playing Bravely Default 47 on the home console but have to go to work, take the game out and put it in your portable, and play it on your downtime or lunch break, etc.
Less development costs because they'd develop one title that works on both the handheld and the console. More third party games because selling to two different markets while having a single development cost. More games since it's essentially a single console. Like the TG16 and TG Express Portable.
*edit*
Also better for gamers because if we have both consoles, we don't have to pay two prices to play the same game. Kind of like Sony's cross buy, but it works with all physical games and all digital games. Since Nintendo now has their NNID which allows one Wii U and one 3DS to be tied to it. So they could have the Fusion NNID and allow one of each Fusion console to work on it.