You have to admit that Perfect Dark's weapons were a lot more interesting. Things like the Laptop Gun and the whatever-the-hell gun that could snipe through walls. (Seriously, what could be more badass than a laptop that turns into a gun that turns into a sentry gun?)It improved nothing in gameplay terms (besides that neat item selector that appeared if you held the A button, but even then it was better to just pause the game). There were new weapons but nearly every FPS has new weapons.
Then there was the multiplayer mode, which added a hell of a lot of options, including bots.
Maybe a better question would be, what did Goldeneye do better than Perfect Dark?