In regards to disney/nintendo relationship, I've never heard anything to suggest they are at odds with each other (not saying that it's not true - just that I haven't heard that to be the case, I've heard the opposite). There was a rumor swirling around last year that Nintendo and Disney were negotiating a deal for movies, but then that fell quiet. Then just back in February there was apparently a powerpoint slide going around from a research investigation on behalf of Hasbro to get an idea of what Mattel has been up to. While the PowerPoint focused mostly on toys, apparently one of the slides mentioned that Disney and Nintendo were coming together to create movies - whether that means movies that exclusively feature Nintendo characters or just something like Wreck-it Ralph is beyond me. Not that you can put that much stock into that, I have yet to find the actual slide, so could just be a fake rumor, but now that Nintendo is making noise and putting it out there that they will be making movies I could see this being true. The director of Wreck-it Ralph also recently stated that he wanted Mario in the original, but Nintendo didn't allow it, but now that they have a better relationship it is possible that Mario could be in Wreck-it Ralph 2.
As far as Nintendo movies in general, I really hope Nintendo aims high. Hopefully they are looking at Pixar/Dreamworks level of quality (Pixar is probably in a league of their own but you should get the point), and not what has been done for Pokemon.
here is the translated interview for anyone who wants to read (from a popular gaming forum)