Genius Programming: The game was way too big to fit on the N64's hardware, so what did Factor 5 do? They used the cartridge itself as ram, essentially streaming the data it needed! Also, instead of using standard microcode (what controlled the graphics hardware), they wrote their own to focus on real-time lighting and high polygon count.
So Ok Its Average: The game wasn't bad, but critical consensus was that it wasn't great, either, particularly due to difficult and imprecise controls. Indy had to stop moving to use the whip, which was also incredibly slow to use, making it almost useless in a fight and difficult to use on puzzles and obstacles (especially when you had several whip-swings in sequence and they had to be performed quickly). And the boss battle at the end requires you to use the whip to injure Marduk. Considering the what it followed, Infernal Machine was a step back.
That One Boss: Marduk. The whip is incredibly difficult to use in combat as it is, because Indy has to stop moving to remove it from his belt and uncoil it. This makes you incredibly vulnerable during this time, as you're unable to avoid Marduk's attacks. It's only compounded by already problematic controls, which makes it difficult to keep Indy pointed in the right direction during a fight. All of this combines to make him an even bigger challenge than he already is.