I've always felt that Perfect Dark was superior to the original Nintendo 64 GoldenEye 007 in just about every way. However, a recent poll from this site concluded that most of our readers favor the James Bond-inspired shooter over its spiritual successor. I fully acknowledge that GoldenEye was a landmark title in several ways, mainly in breaking the Doom mold of "just kill everything on the map" and beginning the trend of more tactical shooters we see today, such as Half-Life 2. However, Perfect Dark built on those early achievements in such a fashion as to eclipse its ancestor in more ways than one.
First off, Perfect Dark is just a better looking game, and not just in terms of graphical quality, although it did push the N64's hardware to the max. It featured settings ranging from a downtown skyscraper to a tropical resort to Air Force One to an alien spaceship, compared to the dull (by comparison) levels of GoldenEye, which consisted of mostly urban/industrial settings. Perfect Dark was also a little bit more challenging overall (the Carrington Institute stage being the crown jewel in that regard) making for a more rewarding experience. While the story might have been a little silly, it's coherent enough to be acceptable in what isn't a story-driven game, and the addition of voiceovers and a more fast-paced soundtrack made things a little more immersive. The introduction of the co-op and counter-op modes, the latter of which can be thought of as an early predecessor of Left 4 Dead's versus mode, made things all the more sweet.
There's a lot more variety in weapon design too. Going beyond the standard 90s style guns of GoldenEye, the sci-fi theme in Perfect Dark led to a lot more creative freedom, resulting in several deadly gems. Perfect Dark gave us devilish little contraptions like the Laptop Gun, the Dragon, the RCP-120, and the Slayer. The addition of secondary fire added some great new dynamics to the weapons, such as the Dragon's proxy bomb function, the Laptop Gun's sentry placement, and the RCP-120's cloaking device. And of course, what Perfect Dark discussion would be complete without talking about the Farsight, the über-cheap sniper rifle that Halo players have dreams (or perhaps nightmares) about?
Perfect Dark also featured a number of technical improvements. Several flaws with enemy AI and abilities were addressed, namely guards now being able to see over railings and their use of melee attacks in close quarters. Motion blur was also put to good use, distorting the screen if the player was hit by a melee attack or a tranquilizer shot. A lot of replay value was added through the combat simulator, consisting of thirty multiplayer-style matches against bots with custom rules. These are great if you want to either practice your multiplayer skills or are just up for a challenge-I spent many a evening trying to finish enough challenges so I could unlock that damn Pelagic II guard.
So in a nutshell, Perfect Dark built on everything that had been accomplished in GoldenEye, and the result was a superior product. Perfect Dark can be thought of as GoldenEye's real sequel, rather than any of the titles released since then under the GoldenEye name. Now, without further delay, feel free to tell me how wrong I am.
I agree, Perfect Dark was a better game. But...
(I'm going to assume right here that the majority of people who played Perfect Dark had already played Goldeneye. This might not be true, and if it's not then I'm wrong in my conclusions.)
Perfect Dark was better than Goldeneye. Giving it benefit of the doubt, assuming you can boil down a subjective experience into a quantity, it was around 50% better. Goldeneye was about a million percent better than any console FPS that preceeded it. Given that, we can assume that people rate Goldeneye high because it solved so many of the existing issues. It was a revolution, not an evolution.
Compare it with Ico vs. Shadow of the Colossus. SotC often gets a higher ranking and I believe part of it is that it's a much better game (with both evolution of style and revolution of mechanics), and part is that about three people played Ico.