Which to be honest is the same as with Xbox Live at this point. Wanna play Bad Company2? Create an EA account or link your gamertag to create an EA account.
I guess it will be the same or similar story here.
Hell ubisoft even created its own set of achievements outside of the gamerscore with Uplay.
The difference is that Nintendo is giving the publishers the opportunity to establish their own systems, Live doesn't have Steam or Origin. It has several benefits for publishers and Nintendo:
1. Nintendo can continue its conservative online approach in its own games, which I believe is something which they are not willing to change
2. Publishers will probably gain much more profit through this, compared to paying Microsoft
3. Nintendo doesn't need to manage the whole online themselves, they will need to bother with the hub and providing a solid infrastructure to enable deployment of 3rd party systems.
it has several benefits for the users as well:
1. They will have option to choose different types of online systems, say one may prefer the online experience EA provides for BF to that Activision provides for CoD. Option for different tastes.
2. This will almost certainly be free and everyone will pay only as much as they needed, probably won't be badgered with ads at least not in the sections Nintendo provides.
3. Competition between different publishers will lead to better experience
4. Online will be suited to the type of game
5. Developers may be able to provide cross platform multiplayer support for their systems,
what I can think of which gamers may not like:
1. smaller games by independent developers may lack adequate online
2. customers need to adapt to different systems, won't be as intergrated as Live
3. it may lack a universal achievement gallery