As simple of an answer as you're going to get, it's just that third party games simply don't sell well on the Wii U.
Even if we were to take into account the Wii U's relatively still low install base and how it still doesn't really sell to well, it still is big enough to support third party games. The PS4 and Xbox One, at the same install base of the Wii U, had third party games selling well.
Almost every third party game on the Wii U has just not sold well. Even the games that were good versions/even the best versions all failed to sell well. Splinter Cell: Blacklist, Call of Duty, Injustice, etc you name it. ZombiU, the premiere hyped third party game for the Wii U when it launched, still has not even sold a million.
Developers like Ubisoft showed a lot of support for the Wii U at launch and gave it plenty of chances with no return in profit, so why should they keep supporting it when nobody is supporting their games?
Now, i'm not talking about all Nintendo consoles here. I believe that third party games CAN be successful on Nintendo consoles, but on the Wii U I have no idea why people aren't buying third party games.