GoldenEye 007 
Perfect Dark Overall Comparison Based on the fact that many people rave about Perfect Dark, I am well prepared for the counter-argument.
My basis for this comparison revolves around the multiplayer aspect of 007. Both games single-player scenarios are great and I simply cannot say that one is better. However, 007 offers, for the first time a chance for a group of 4 to run around killing one another. It not only was the first but it also setup a framework for how games should do it in the future.
Perfect dark of course followed this frame work, but really didn't improve on it. Sure the weapons were cool, but the levels were no match. (To this day I still think the Complex is the best battleground made). Perfect dark broadened the scope of options, but failed to take any deeper.
Ultimately, if I had 3 other friends sitting in the room, I'd much rather play 007 than perfect dark, maybe for the shear nastalgia, and that in itself is justification.
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Also, a quick note: A lot of times, I've heard that people didn't like Perfect Dark because it had "bad graphics" and lagged. It took me a while to realize that a lot of those people were playing without the RAM expansion included with the game exactly for that reason.