Like everyone else who was playing video games in 2000, I logged many hours playing Perfect Dark on the Nintendo 64. But, like many others I'm sure, I never played the Perfect Dark game released for the Game Boy Color. I'm going to put your mind at ease now and tell you that you didn't miss anything by not playing this game.
As in the console version, the Game Boy game puts the player in control of Agent Joanna Dark on a series of missions, the details aren't important, that are completed by shooting a lot of people. Unlike the console game, this version uses a third person overhead view. The controls for the portable game don't feel as instinctive (as instinctive as killing hordes of people can be for gamers who don't leave the house if they can avoid it). Reloading and picking up items are more of a hassle. Game movement is slow and clunky.
Most importantly though, this Perfect Dark lacks the multiplayer mode that was the bread and butter of the N64 game. No one played Perfect Dark alone if they could help it. Why on Earth would they want to play Perfect Dark alone and on a tiny screen?