The solution is simple: take out all assets from the game and make an utility to exctract them from n64 rom, which you must provide yourself. That's it. Nintendo can't DMCA you anymore and the project becomes completely legal.
The code is still an asset.
It is not like someone watched the game, saw acceleration was this, jump behaviour was this and remade it in their own code (if you want to go further see something called clean room reverse engineering). The code was taken from the ROM itself, that it went via a decompiler is immaterial in this.
At very best you could try some kind of interoperability claim (most law has provisions for this one) but that is still something I would expect you to have to argue, and argue hard, in court.
They would still have trademarks on their side as well, and while there are workarounds for that from what I have seen none of them are employed.
albeit it is the correct move to shut it down, this is not piracy as there was no official port of 64 on pc, nor this is a game emulating the console using the directly ripped rom, The code used is not nintendo's code. calling this piracy is equivalent to a programmer writing a commonly used function and calling it piracy because the compiler's end result is the same. As the original code was never a copy (in fact, its probably not even a byte for byte copy either, because nintendo never set the original compiler optimization flag on 64, and this project probably did)
the end result is like piracy that it in the end goal gives 99% of the same experience as the original version, but the creation of it was not piracy at all because there was no code to copy in the first place.
The infringement is keeping the trademarked assets in the game, and not the game itself. If the references to every trademarked thing was removed, but the gameplay mechanics were the same, the project would probably be deemed legal.
It is Nintendo's code. A decompiler does not pluck code of thin air but directly reads the original compiled version and recreates it from fairly direct (no real creative input, not that it matters for the purposes of clean room reverse engineering) methods. Functionally it is no different to say stripping the comments out of the code and then declaring it your own, or disassembling the ROM and calling it your own. Decompilers themselves are some of the most interesting and creative pieces of code I have ever seen but the results of using one are a different matter.
Most copyright also makes use of a concept like substantial similarity -- I can't go to an art gallery of a painting made last year, take a picture, make it black and white (never mind say tweak a red to be slightly more vibrant) and sell a million copies.
Official PC port, or lack thereof, matters not one bit for anything -- in some instances, say hardcore industrial gear used only by super high end professionals, when discussing trademarks you might argue that no customer would be fooled but in this case Nintendo would just point at the long list of clueless grandparents, parents and the like buying games for their kids as a primary customer and at that point you might not be sanctioned but the waste of time making that argument would be noted by the judge and likely any jury you just made it in front of.
Equally while I imagine some assets might be trademarked (say the logo and name), or some kind of trade dress or noted colour scheme (the red and blue of mario perhaps) in those places with such protections it is the copyright that such things will mostly be concerned with when the game's assets are the thing in question.
probably renews every time they release it on a new console, so last version was on the wii i think at least officially
Any extra creative work would gain additional copyright for the full duration. The previous releases are still within the same timeframe they originally had -- you can't string things out infinitely.
The usual example given of this sort of thing is public domain books, this is to say books of works long out of copyright. The text itself might be public domain but the typesetting (if you have ever written a document and then had to go back through to make sure it all lines up, new pages where you need it, contents page and whatever else you know how much as a pain that is), font used (assuming fonts are copyrightable in the jurisdictions concerned), any preface added and so forth mean you likely can't just photograph all the pages of your new rerelease and share them with the world, though you can OCR the original work from it all, stick it all together and go from there.
In some cases it is also why some galleries don't like you taking pictures of their old paintings (US wise this year saw works from 1923 hit copyright free status
https://web.law.duke.edu/cspd/publicdomainday/2020/ ) as they might be making money from selling reprints and if they own all the best/only scans already...
This can make things harder if originals are hard to come by to scan back in, dump or otherwise digitise but I don't imagine that will be a problem if the ROMs are already known.
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