Where do the Third Party/Nintendo fan issues come from?

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KungKras said:
It didn't start with Nintendo and it didn't start with third parties.

It started with Atari.

Not the answer you expected maybe but let me explain. Atari had flooded their system with crap the previous generation. Which led to consumer confidence being eroded to the point where the home console market was declared dead. Nintendo looked at this and put in severe restrictions on their platforms to prevent this from happening in the future. This of course upset third parties.
When the playstation swooped in, Nintendo didn't catch on time that third parties and the playing field had changed. Sony reopened the floodgates for software at the right time and caught Nintendo off guard. And they never recovered since.

But that's only half of the truth. Nintendo made the same mistakes in Japan with Famicom, by not having a lockout chip, unlike NES, and it was a huge market of unlicensed Fami games (which may be why Nintendo promoted the Famicom Disc System so heavily). Whether the restrictions were there because of seeing what happened to Atari or Nintendos own experience in Japan, unlicensed games are games you did not pay royalties for he platform holder. 3rd parties (like EA) liked it, but not Atari/Nintendo/Sega. 

Had Atari wanted to prevent all the shovelware from crashing the market, by the time of their crash, Atari could not do anything about it.

But, about the third party games on Nintendo systems, the handhelds haven't experienced problems. The only issue here is money and having the royalties cheaper.