I don't think third party publishers/developers truely "dislike" Nintendo being that they still have shown a ton of support for both the Wii and Nintendo DS ... I think third party publishers did not expect Nintendo to be successful with either the Nintendo DS or the Wii because of how Nintendo's strategy went against conventional wisdom.
Although few publishers and developers would phrase it this way, a lot of people in the industry believe that people who buy videogame consoles instead of gaming PCs do so because they are less expensive and easier to use than a PC; and these gamers secretly want the same experience that PC gamers want. In other words, they believe that everyone wants complicated gameplay mechnaics, photorealistic graphics, and fully featured online multiplayer.
Now there is some truth to this because a lot of former PC gamers grew tired of constant upgrades on their PCs, moved to consoles, and are looking for the same kind of games; and there has always been a certain demand for a PC styled gaming experience on consoles.
What many publishers/developers missed over that past several years was that, although the console gaming market as a whole was growing, there was a massive shrinkage in the videogame market among certain demographics and no growth among others because this push towards PC styled gaming was alienating many potential gamers.
The industry (on the whole) has not adapted and does not understand what to do with the Wii, they have made assumptions about what Wii owners want and produced products to match these assumptions and do not understand why they have not been that successful. They have difficulty understanding that someone who doesn't exclusively buy First Perso Shooter games may want to buy a First Person Shooter game on occasion, and that a gamer who owns a PS3 or XBox 360 may also own a Wii. They also have difficulty accepting that a person who may not value the qualities they associate with a quality game will not (neccessarily) buy an awful game simply because they market it to them.
This problem has been compounded because their "High Quality" developers have been tied up in HD projects, in many cases since before the Wii launched, and when it takes 2 to 3 years to complete a HD game and 1.5 to 2 years to complete a Wii game there is a massive turn around time from publishers/developers seeing the need to support the Wii heavily and the Wii receiving this support.
