Nintendo has a history of CnD'ing publicly distributed Fan Games. Being protective of their IP, any unofficial game that's using pre-existing assets available for downloading or torrenting will likely be taken down. Yeah it sucks, but my question is, why is it only Nintendo getting singled out? This is actually standard with most companies. It's not just Nintendo, the vast majority of game companies take legal action against unofficial fan games. Microsoft for example, shut down a Halo Multiplayer fan-game based on the classic style. Square Enix has shut down quite a few Dragon Quest and Final Fantasy fan projects. The only notable exception to this, is Sega with Sonic the Hedgehog. But that's only because Sonic Team is so incompetent with the series, that Sega is willing to make an exception for it. So this isn't a Nintendo only problem, it's an industry-wide problem. Video Game Fan works just haven't been recognized as a viable hobby yet, so until some agreements or laws change, companies can and will take legal action. Like I said, it sucks, but it is what it is.

So do most gaming companies. It's just that Nintendo's IP is more iconic, so fan games pop up more often there.

I just gave you two notable examples, Microsoft and Square Enix, who also shut down fan games and mods when they pop up. Nintendo fan games are more common, so they get more coverage.

Should they not be consistent?

If they weren't, that would open a whole other can of complaints from people.

In my opinion, they should be protective of their IP. That is how their franchises have kept their value and stood the test of time.

Why not use your energy and talents on something of your own (comment for game makers)?

Like I said, Nintendo fan games and mods are much more common, so they get more media coverage versus other companies. But that doesn't mean other companies don't take legal action most of the time.

Because when 1 Sony's or MS's fangame birth, 50 fangames of Nintendo pops too.
Just see Pokémon, i'm not a fan (lol) of fangames but i can said to you easily 15 fangames when i was never played at their.

Because Nintendos IP gets the most fan projects. By multiple miles.

That is because people care way more about Nintendo and Nintendo-fans are way stronger emotionally attached to the IPs than to most of the other stuff. That why such decisions are met with more publicity and I guess there are more such fan-projects to talk about to begin with. Just compare how many IPs Nintendo has and how many Sony or MS do have.

Sure, that's probably correct.  It also answers the question in the OP.  People focus on Ninty being IP Nazis because Ninty is doing it all the time.  It may be the case that MS, Sony, SE, and everyone else would do it all the time if there were a constant stream of fan games using their characters.  But, there isn't a stream of games for them to shut down, so they don't shut things down.  

In other words, Nintendo is doing it all the time, so people are calling it out all the time.  

Also because the game creators don't take the step of changing the game and getting outside of the copyright imo.

That group making the My Little Pony fighting game got CnD'ed by Hasbro, but they just changed the character designs to something unique and re-wrote the plot of the game, changing nothing about the gameplay. I realize it's no small feat to change a lot of assets, but it's the creators choice to let the game die because they won't change things to replace NIntendo copyrighted stuff with original ideas.