The Amiga had planer graphics modes, while the PC/VGA cards had chunky mode (in 320x200x256 color mode).
It means that, to set the color of a single pixel on the Amiga, you had to manipulate bits at multiple locations in memory (5 in 32 colours), while for the PC each pixel was just one memory location; In chunky mode you could just do something like: videomem[320*y+x]=158 to set the pixel at (x,y) to color 158, where videomem would point directly to the graphics memory (at address 0xa0000) -- It really was the simplest graphics mode to work with!
If you just copied 2D graphics (without scaling/rotating) the Amiga could do it quite will using the blitter/processor, but 3D texture mapping was more challenging because you constantly read and write to individual pixels (each pixel potentially requiring 5 memreads/writes on the Amiga vs. 1 on the PC).
Doom's wall texture mapping was affine, which basically means scaling+rotation operations were involved. The sprites were also scaled. Both operations a problem to the Amiga.
As software based 3D texture mapping games became the new hot thing in 1993-1997, the Amiga was left behind. Probably wouldn't have been a problem if the Amiga has survived until the 3D accelerators in the late 90s.
This is quite well described elsewhere. Google is your friend if you want to know more! :-)