I'll just leave this here:
In the US, at least, companies are under no obligation to do what Nintendo did to KBM and Prism. They just decided to do it. This myth gets dragged out everytime something like this happens, and the corporations love it because it keeps the blame off of them and the fans off their backs.
Okay, so, full disclosure, I made an account here because I was searching on info on Prism, and I am a complete and utter butt who very much has an interest in law.
And what you said is wrong.
US Trademark law does very much require corporations to defend and actively pursue infringing use of their own registered trademarks, as well as actively use the ones they own, lest they lose them and become genericized, see Aspirin (Used to be a trademark owned by Beyer, lost when they let other companies use it, still own the trademark in many EU countries.)
The article you linked was in regards to speech on the internet, not other products that were using the trademark. The First Amendment does indeed trump Trademark law, but the First Amendment does not cover commercial, or even non-profit, products.
There is also very much a legal precedent for Nintendo, under US law, in this case, see 2013 case "Abraham v. Alpha Chi Omega" (Forbes did write an article summing the precedent up as "You snooze, you lose" because of the Laches doctrine.)
Lastly, a nice quote from the April 2011 Report to Congress "Trademark Litigation Tactics and Federal Government Services to Protect Trademarks and Prevent Counterfeiting"
Trademark owners have a legal right and an affirmative obligation to protect their trademark assets from misuse. If the owner does not proactively police the relevant market and enforce its rights against violators, the strength of the mark, the owner's ability to exclude others from using the same or similar marks in the marketplace, and the value of the asset all will diminish.
Failure to take action may result in consumers being confused or deceived as to the source or sponsorship of goods or services, harm to the owner's reputation, and lost sales. A trademark owner is not required to object to all unauthorized uses that might conflict, for not every third-party use poses the same risk of eroding distinctiveness in the marketplace.
However, widespread unauthorized uses may cause the mark to lose its trademark significance altogether and fall into the public domain. Thus, diligent enforcement of trademark rights is necessary to help prevent others from unfairly trading off the mark owner's goodwill and reputation and to protect the public from mistakenly believing that the mark owner authorizes, endorses, sponsors, or is somehow affiliated with another business.