It's hard to say and possibly impossible to guess.
I believe the only Nintendo games that most people know and sale well in consoles recently are the Mario games, Zelda, and Smash Brothers but these usually come out once every generation (except Mario Party). Wii games are debatable (look at their success for Wii U currently) and probably impossible to recreate if Nintendo has no say in the controller development for other consoles.
Niche Nintendo games like Pikmin and Metroid (even Kirby) would probably sale horribly since they are niche in nature and hardcore Nintendo fans are probably the only ones that buy these games. This is especially true if Pikmin/Metroid stay exclusive to one console. It will split these gamers if they like more than one of Nintendo niche series and choose a console that has the more appealing one. Most of these hardcore Nintendo fan have pretty narrow tastes and do not want to buy a new home console that costs more than 300$ even if they have good third party games. I'm aware that there are the old Nintendo gamers that support their current games while owning Microsoft and Sony systems, too, but how many do those exists compared to the hardcore Nintendo fans outside of the internet? Maybe if Nintendo gets rid of their kiddie image than other people would accept these niche series. Even then, the gameplay of these niche games are different and way more mild compared to the popular games sold in Microsoft and Sony systems. Star Fox and F-Zero could possibly do better if they are ported to every console because their violence and grittiness could increase without ruining their identity. Same with Zelda I guess.
I guess Nintendo can make a new IP or series to attract other gamers that don't like the typical Nintendo games being Mario to Metroid. But why would they start doing that now when they can't even make a new successful IP (Pikmin) or a modernized version of their older IPs (Metroid Prime) since the GC? Donkey Kong Country Returns doesn't count because non-Nintendo gamers probably see it in the same Nintendo genre and gameplay like 2D Mario games.
With that said, it's still hard to guess if Nintendo would be better of as a third party. I'm sure I probably haven't thought of many postives... It's a topic that could be as controversial as Apple licensing their OS to other PCs to gain more profit.
Sorry for any grammar errors and run ons sentences. Typing this late at night.
