I can see that situation, but i dont think that 3rd parties will drop WiiU developement because they cant have Nintendo IPs in their games. Unless i misunderstood what you ment?
No, that's not really what I mean. I mean that Nintendo's focus as a publisher first, hardware maker second sometimes makes them a little adversarial with 3rd parties. I imagine that EA wanted too much control over Nintendo properties or perhaps too much of a slice of digital sales for Nintendo's liking which made their online plans fall apart. The CD add-on situation was definitely a case of Sony wanting too much control over Nintendo's properties but that still could have been handled better by both sides.
I'm not really sure what Nintendo could have done really in either situation but I think being such a successful publisher places them in an odd situation when dealing with other 3rd party publishers.
I do think that working with smaller independent studios like Platinum is a good idea for them. If the games they work on together are successful it could start to build a foundation that leads other independent dev houses to see Nintendo as a viable partner.
Edit: Just to make things clearer I'm not talking about a situation where hypothetically EA wants to make Battlefield:Mushroom Kingdom, I'm talking more about a situation where let's say EA wants to co-publish 3D Mario with Nintendo because of their theoretical online intergration with WiiU.