You can dodge the trademark aspects (part of that would be not using the same, art and whatnot. See why a lot of things on
https://osgameclones.com/ will have a different name and get you to use assets from the original game). Still got the copyright thing on the code to worry about but the trademark stuff is able to be dealt with.
As far as point.
N64 emulators are more or less limited to N64 type hardware. PC ports then can far more easily (as in what I super skilled N64 hacker, for which I reckon there are less than 10 in the world as the N64 was a flop and maybe 200 that could cross skill from a similar setup over a few months with a few more on a longer term path still, could do in months of serious effort a moderately skilled PC coder could do in a weekend, and kids that can just about press compile can also do a few limited things that they would have no chance of doing even with something said said seriously skilled hackers made into a nice program).
This would include
Higher resolution, beyond anything the texture replacement stuff can do.
Higher framerate
Higher draw distance. I know fog at times is part of the aesthetic but you can still keep that.
Easy mods to all manner of things
Huge levels, most of which can be made to have all manner of other interesting things.
Easy control remap, assuming it is not made inherently as part of the port this is something the "can press compile" person can do if they care to read through the text based code and change something, add things together.
Easy AI control and remaking -- rather than boring "rush towards you and attack" (or marginally less advanced than that) you can make it a bit more tricky.
Far easier translations -- I know we have seen Arabic for Zelda 64 now but it required someone use the French and a horrible bodge job to get right to left text.
Custom music as easy as copying a MP3/midi file into the directory. Want all those Legend of Zelda reorchestrated things in the game instead of bleepy bloopy N64 sound? OK then. Want Zelda hardcore death metal edition? OK then.
Voicework if you wanted it to go along with text (text by itself will have things to start and stop whatever voice work you want to add)
Multiplayer setups become reasonable -- having a second player appear on screen, or several hundred with attendant increase in enemies and pickups, is reasonable to do on a LAN at least (
https://www.gamasutra.com/view/feature/3374/the_internet_sucks_or_what_i_.php?print=1 ).
Minigames expanded out into more complete games where doing that as a N64 hacker would be a serious effort. Same for a boss rush.
Fixing bugs. If you wanted to I reckon the kid that can press compile can probably sort the final boss bottle bug so that bottles no longer reflect things, and probably quite a few of the things I see speedrun types (ab)use too.
Remaking Master Quest but tweaked to however you like if you wanted to go there, indeed whole new game in the Ocarina style becomes a fairly doable thing (granted I would probably still go for a new engine rather than something old like this even if there was not the copyright issue hovering over my head).
Ports to things that are never going to run a decent N64 emulator (see all the things Mario 64 got ported to, in addition to everything above then most of those are not going to have good N64 emulators any time soon, if ever).
This is all just scratching the surface.