I wouldn't call it a 'bad' relationship per say, its just currently we all know that Nintendo systems tend to sell WAY more first party software than third party software
of course the likes of Ubisoft are going to be willing to risk a little cash to put some exclusives on a new Nintendo system, especially because there was uncertainty of if the Wii U would be a hit like the Wii
it'll happen again with the NX. you'll have some third party developers willing to put some effort forth at the start and then DEPENDING on if the NX takes off more will come or go
there a number of significant third party software developers who actually have sold a lot of games on Nintendo systems over time, especially handhelds. the likes of Capcom, Ubisoft, Square Enix- are not going to risk permanently damaging their relationship with Nintendo because they're annoyed about the lack of a short term good connection and results
one could blame Nintendo SLIGHTLY- generally going with the goofy gimmicks and less advanced hardware (spec wise) means that its less likely non-Nintendo casual gamers are going to hop over and buy from third parties
I think third party software sales would obviously skyrocket up in sales on Nintendo systems if they just would release an extremely competitive spec system. I mean lets face the reality here, the likes of Activision, EA, UBisoft- they make a lot of the same sort of action and sports games over and over. pretty much all of their software caters to a high spec console that the 'mountaindew' sort of gamer enjoys
so for the third party and Nintendo relationship to flourish NIntendo simply needs to get on board with a more streamlined higher spec system. no goofy controller either
at this point I think a lot of Nintendo fans want Nintendo to just go back to the traditional sort of console and controller as well
at any rate I wouldn't call the relationship 'bad' at this point as a lot of the third parties have sold lots of software on the 3DS and sold LOTS of software on the DS/Wii last gen
