I'll see if I can find a link to an article that can explain it.

http://nintendoenthusiast.com/article/wii-u-third-parties-mistakes-new-beginnings/

http://nintendoenthusiast.com/article/nintendo-and-third-parties-a-rocky-rainbow-road/

Anyone who thinks Nintendo and third parties don't mix obviously never heard of Nintendo 3ds. There is just no money for 3rd parties to be made on Wii U. Simple as that.

Ubisoft jumped onto the Wii U because they believed it would have been a commercial success since it would have followed the Wii, in fact their games in the last few years almost never appeared on Nintendo consoles, same goes for EA...

bringing up handhelds is a good point.

sony has great 3rd party relationships in general but that didn't help vita.  there was some 3rd party support there at launch and it very quickly evaporated as the sales numbers came it.  losing 3rd party support on vita was absoultly brutal towards accellarating the collapse of vita being a "viable platform" but i'll restate the same thing i've written here time and time again:

it is the platform owner's responsibility to make an attractive platfrom for 3rd party developers not 3rd party developer's responsibility to make the the platform owner's hardware attractive to consumers.

nintedo is to blame for wiiU.  sony is to blame for vita. 

There are so many titles missing from 3ds third party support it's crazy. Kingdom Hearts, Street Fighter, Dead Or Alive, Metal Gear (Snake Eater remake), Splinter Cell, Ghost Recon, Devil Survivor, Etrian Odyssey, Fifa, Madden, Pro Evolution Soccer, Samurai Warriors, Lego, honestly the list goes on and on. 

Maybe there was a bad relationship between Ninty and Square back in the day, but I doubt something like that is happening nowadays.

I think Nintendo likes having a platform dominated by their own software and not having to compete with the mainstream 3rd party titles.

NES, GB, N64, Wii, DS all averaged about 40% of total software sales coming from Nintendo-published games and averaged about 40 Nintendo-published games to surpass 1 million units sold. On the other hand, SNES & GC are the two Nintendo devices with the largest amount of multiplatform titles and Nintendo-published titles only make up about 25% of total software sales with only 18-25 million selling Nintendo titles.

U could argue that this shows when Nintendo devices get the mainstream 3rd party titles that their own software sales take a hit and I don't think Nintendo wants that. The type of 3rd party support they want are games that will compliment their own software and games that are exclusive.

It's always a two way street. Nintendo didn't care about 3rd party (or else they would've designed Wii U with their input in mind) and 3rd parties didn't care anymore because it became a hassle instead of an opportunity to sell more.

Sony and MS did the right thing by creating a platform FOR 3rd parties instead of just creating a platform and then trying to force everyone on it.

Because they sell horrible on Nintendo platforms.
GTA, Call of Duty, Fifa etc. sales proofed this.

3rd partie games which are not exclusive don't sell all that well on Nintendo consoles. So third parties don't care about Nintendo. Having odd hardware in comparison with Playstation and Xbox One doesn't help either. But perhaps NX will change that even though Nintendo put quite som effort in being the best secondary console for the masses by doing their own thing.