Nintendo will always fight an uphill battle with third party developers, aside from Nintendo's terrible past of basically pissing on third party developer, Nintendo currently expects them to act like mature diplomatic companies and work within the confines designated by common place business, which is perfectly fair and honestly the way it should be as it encourages competition and innovation, but developers don't like this. With the PS2 and Xbox, developers had free reign to do what they wanted, now that they see this era comming to an end with the uncertainty of the PS3, the limited appeal of the 360 and the popularity of the dreaded Wii, they're struggling to keep the good ole days of the PS2 alive, but are failing.
Basically the third party Developers are like kids who don't want to come in from Recess to sit down in a quite structured classroom. Eventually they're going to have to concede and go back to school and play by the rules, but they're not going to like it, and you better believe they're going to give the teacher (Nintendo) shit.