You'd rather use the four C Buttons to aim? Controllers don't exactly have a lot of options. Sure, the most accurate option is "trackball," but those were only on high end arcade cabinets and PCs at the time. Couldn't get any of them for under $300 USD. And lightguns woyld have needed more inputs on them than they had at the time, not to mention the N64 never had a lightgun peripheral for it to my knowledge.
Too bad the N64 mouse only launched with the 64DD in Japan then. Either way, GoldenEye could never be played with a mouse back then. It only took someone creating a special build of an emulator to get it to support it only within the last like 5 years.