Agnes doesn't help much with 3D acceleration. It has a blitter which is capable of filling polygons, but they must then be copied in to the display bitmap so it's actually slower than just filling with the CPU. Additionally the blitter requires the horizontal limits of the polygon to be rendered first, meaning an additional line draw per vertex.
The biggest performance limitation for 3D on the Amiga is memory bandwidth. In fact all 16 bit home machines of the time were the same, memory bandwidth was the biggest challenge.
The maximum fill rate can be achieved by using unrolled CPU loops that write directly in to bitmaps. There is then no copy stage, and no need to line draw vertexes.
The general strategy used by most high performance 3D on the Amiga is to calculate all vectors in one go, allowing as much data to be kept in CPU registers to avoid memory reads. The display is then rendered by the CPU alone as outlined above.
Since the Amiga had the same CPU as the Atari ST running at a similar speed, but with actually a little bit less memory bandwidth performance was about the same. The Amiga could do some tricks to improve things, such as variable colour depth on different parts of the screen and sprites for low overhead overlays, but in practice they tended not to be that significant performance-wise.