RE4 isn't really an early 3D game. It was a late GameCube title almost a decade after Quake.
There has been some 2D decomps too, Pokemon Red/Blue being the biggest I can think of. I can also imagine they make more sense for the 3D consoles where games tended to be written in higher level languages than raw assembly.
True, not the earliest gen. But it's a 2001 console (not 2004) despite this being a 2004 title.
GB games are written in assembly, so decomp means marking sections as code or data, then commenting the crap out of it. The earliest Nintendo consoles to use C were the N64 and the GBA.