A loved GE back when it came out. But it was always going to be hard for any game following it because it represented firsts for so many people. Their first FPS, first 4 player multiplayer and it was an amazing licensed game at a time when most associated licensed games with being throwaway. We'd come a long ways from LJN. But I think even if you gave someone who never played GE or Nightfire both games that they'd come away feeling like Nightfire was the better game. Even if you were to give them a version of GE that fixes its performance issues (it's super rough, especially in multiplayer). As you said, it's just a better game in every way.
I loved Goldeneye as a kid and I definitely appreciate what it did for gaming in general. But like Alone in the Dark and horror it has aged extremely bad. I played some Goldeneye this summer and it was rough. I would love to go back and see what I would think of Nightfire today, probably outdated in some ways but I think it would at least still be solid.