Maybe!

Probably not though.

First you must verify the bolded. Is this true? 

He has nothing to be scared of. He has a gigantic fan base that would watch him play anything. Besides he pretty much only plays small indie games lately and indie devs dream about Pewdiepie playing their games. He has nothing to worry about, he's just speaking on behalf of let's players because he's the biggest one and because his voice is heard.

It cannot be proven, obviously.

But with youtube creators boycotting it......

Of course he doesn't. That was never the issue. It's the people who desperately try to take the attention off Nintendo shoulders, who want to make it the issue.

Felix himself clearly said that he intended to speak FOR others. The most prominent youtube gamers; AngryJoe, TotalBiscuit, Boogie and PDP have all said the EXACT same thing. Felix is just easy to attack and divert attention from Iwata's laugh inducing decisions.

The only two parties (negatively) affected are nintendo centered youtubers and nintendo.

I really don't like when people use the words "free advertisement" for these things, because it's not true. The person playing the game is NOT advertising the game. The reason the majority of people do the Let's Plays and whatever else videos they do is NOT to show off the game. That is NOT the purpose of their videos. If it were, they wouldn't be showing A) The full(or large portion) of the game B) irrelevant voice overs (such as screaming or ranting) and/or C) any potential negative areas for the game.

In the quote I read earlier from pewdiepie is a lot more accurate, it is "publicity" much more than it is "advertisement." Would you consider a bad review for a game advertisement?

People are always overstating the positives with the way things are/were, but negatives are definitely associated with Let's Plays.

This may not be the best choice Nintendo is making, but it has already been stated several times that this is just a Beta. It sounds like, perhaps, Nintendo is open to suggestions.

His channel obviously benefits from diversity. As with any brand there needs to be new content that appeals to the audiences (eventually they'll get tired of watching similar indie games.) And a lot of his viewers likely found him because of said content. From what I've experienced of his channel there are both indie games and AAA releases (The Last of Us, Infamous, Heavy Rain, etc.) Like he said, "There’d be no “let’s play” without the game to play."

Indie developers literally put references to him in their games.

Pewds and other youtube creators do not need nintendo, they can be popular playing anything, and there is so much awesome content out there that you could probably play a million hours without even touching a nintendo. Pewds doesn't even play nintendo games iirc. He's more into pc. He's talking about nintendo because what they're doing is such a big mistake. He's absolutely right, and if publishers want to try and follow the nintendo route, they're gunna learn the hard way.

He's just expressing why he think their new policy is a bad move (while also acknowledging that they're totally in the right for choosing to do it). As he said, it's the Nintendo focused channels that are going to get the biggest slap in the face from this, not him. Nintendo aren't going to generate any hugely significant amount of money from the policy, they're just going to push youtubers towards the games of companies that acknowledge the benefits of the exposure provided (at least relative the alternative).

They aren't though. I can find plenty of Nintendo oriented let's plays. There will be plenty of people perfectly happy to get 60% of revenue (if they accrue viewers), but honestly most let's players do it as a hobby, not for money. They'll be glad Nintendo isn't removing their videos. This only affects the few who do it as a business. 

Look at the number of results (top-right corner.) 

 https://www.youtube.com/results?search_query=let%27s+play+a+link+between+worlds

https://www.youtube.com/results?search_query=let%27s+play+pokemon+x+and+y

https://www.youtube.com/results?search_query=let%27s+play+pokemon+omega+ruby

https://www.youtube.com/results?search_query=let%27s+play+super+smash+bros+wii+u

https://www.youtube.com/results?search_query=let%27s+play+bayonetta+2

https://www.youtube.com/results?search_query=let%27s+play+pikmin+3

https://www.youtube.com/results?q=let%27s+play+wind+waker+hd

https://www.youtube.com/results?search_query=let%27s+play+super+mario+3d+world

vs. 

https://www.youtube.com/results?search_query=let%27s+play+pokemon+black+and+white

https://www.youtube.com/results?search_query=let%27s+play+super+smash+bros+brawl

https://www.youtube.com/results?search_query=let%27s+play+skyward+sword

https://www.youtube.com/results?search_query=let%27s+play+super+mario+galaxy+2

https://www.youtube.com/results?search_query=let%27s+play+super+mario+galaxy

https://www.youtube.com/results?search_query=let%27s+play+zelda+spirit+tracks

https://www.youtube.com/results?search_query=let%27s+play+zelda+phantom+hourglass