My point about the apps is that they're simply putting N64 games on the N64 app. You're saying they have superior versions of Mario 64 (def not superior), Zelda OoT and Star Fox, not a single person expects those games on the N64 app because they're DS and 3DS games. Those will come to their respective apps if/when they arrive.
All of the things you mentioned are not things I ever expected or asked for (was anyone expecting Mario 64 in the Odyssey engine?). My expectations for Nintendo have always been pretty realistic. You named some things you apparently expected and got the short end of the stick. Did anyone expect we'd get NES and SNES apps along with Tetris 99, Pac-man 99 and the NSO vouchers for 20 dollars a year? Cause that's a pretty amazing value to me. Sometimes they disappoint, sometimes they don't.
I think you and I agree on expectations. I never expected those things, but people routinely expect the world from Nintendo, especially when it comes to classics. Nintendo has been consistent on how they treat those games lately. They don't do bargain digital versions of their classic games (like Doom or Turok did). They don't
really do collections either. They either do $60 remasters/remakes (and those are major releases) or they put the ROMs on NSO. I wouldn't expect Nintendo to do full remaster treatment of GoldenEye (even if they had the rights) when the rest of their classic N64 games didn't get that treatment and just got ROMs. But, as you say, MS is making the moves...
The difference between GE and everything you mentioned is that, like you said, there is an Xbox achievement list. It seems like MS, not Nintendo, are the ones making the moves. If Nintendo does in fact have a say, they wont choose an N64 ROM over a GE remaster. MS releasing a game on the eshop is drastically different than Nintendo doing a full Mario 64 remake in a new engine.
This is where I disagree. Nintendo, as a business, has a lot of reasons to prefer the N64 ROM over Microsoft releasing an HD remaster:
1. It sells NSO Expansion Pack. Increasing subscriptions is a clear benefit to Nintendo over selling the title where Microsoft gets the lion's share.
2. Development costs are minimal
3. Online multiplayer and voice chat are already built into the NSO app. We know these aren't great implementations but they will still advertise it as modern and online.
4. They'll sell more N64 controllers (assuming they can make them), and can position this as a strength - get the authentic experience.
5. The number of people that actually care about the difference is small. And how much do they care?
As stated above, Turok and Doom remasters are both on Switch and not the N64 app.
Those aren't Rare games and Nintendo has no claim on them. Microsoft has an Xbox version of Banjo-Kazooie, and Switch got the N64 ROM. This just happened, I don't see why GoldenEye would be much different.