You made a statement about EA's specific relationship with Nintendo and I answered it. Now you want to make look like I'm oversimplifying Nintendo's third party issues. Stop, just stop.
Except that it's not true for EA either. The Genesis got the best version of EA sports games because Sega worked with EA. Square gave their RPGs to PS1 over the N64, Rockstar skipped Nintendo with GTA. EA has been constantly pulling things from Nintendo over the years. EA dropped Nascar, MVP Baseball, NCAA sports from the Gamecube. They followed it up by pulling Tiger Woods, NFS, All Mature Titles (Mass Effect/Battlefront) for the Wii. I'm not sure what happened with EA, but if anything whatever happened simply quickened the effect that was already happening. By the end of the Wii U there never was going to be any EA support without positive interaction from Nintendo.
I think you also simplify it to EA pitching Nintendo and being surprised when Nintendo didn't use them. Nintendo went to EA for online help. There also had to be some sort working relationship with EA for EA to bring as many games as they did at launch. Mass Effect 1 + 2 skipped Wii and they brought 3 to the Wii U. NFS Most wanted skipped Wii and they brought it to Wii U. Yeah, you can argue they torpedoed those releases, but they lost money bringing to the Wii U so they cared enough about the Wii U to put investment to it at one point. Had whatever positive effect not happened, I think you'd have seen Madden 13 and maybe Fifa 13 at launch and that is it (based on their Wii support). Then based on sales they probably wouldn't have developed sequels for those either.
EA knew no one was going to buy the game at full price. Accidental or not, the Origin sale was their best chance to recoup the investment they made porting the game. And I find it gard to believe it was a glitch when the press release for the sale mentioned Wii U as well as other platforms.
If EAs only chance to recoup was to sell the game at a loss, then I still don't know how the sale was a bad thing. And I still don't know how an obscure sale that 95% of the people in the US didn't know about would have a material affect on the total sales for that game. I got NSMB U for $39.99 on sale durting the first month at Target. Did that sale hamper Wii U sales as Nintendo went for initial adopters instead of long term sales? I just don't understand your argument here. Games go on sale all the time.