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It seems that 3D games, especially simulations like Falcon, were not faster (fps) on the Amiga than on the Atari ST - even a bit slower due to the CPU clock.

I was wondering why this is the case, since the Agnus seems to me as an early model of a GPU, capable of drawing vector lines and even fill out polygons. Was it not capable to display the typical number of 3D objects in those games or was it simply not used, since it would require a complete different codeline for the Amiga with respect to 3D rendering ?

There are a few reasons why multi-platform 3D games turned out to be no faster on the Amiga than on other 68000-based platforms without its blitter:

The developers may have targetted the lowest common denominator system and not taken advantage of the blitter when they ported to the Amiga. Early games and poor conversions tended to be like this.

A naive implementation by somebody unfamiliar with the hardware may well fail to use the blitter's line-drawing and space-filling operations efficiently, thus losing the benefit. If one draws and fills individual polygons and then blits them to the framebuffer, that is a lot of wasteful work. AmigaOS itself didn't set a good example here.

Finally, the blitter is a pure 2D device which offers no acceleration for 3D calculations, so the main CPU needs to do those. This involves a lot of matrix multiplication, and the 68000's MULU/MULS instructions are very slow, taking about 70 cycles. (The exact number of cycles is data-dependent because the microcode uses an iterative algorithm.) At 7.09MHz that's a shade over 100,000 multiplies per second, or 2,000 per 50Hz field. Even if the blitter was infinitely-fast, this still sets an upper limit of a few hundred points on screen or compromise on frame rate.

The thing the Agnus has that speeds up 3D games is the polygon fill feature. Blitting by itself is not so much a standard operation driving 3D performance. It can help 2D games and windowed GUIs a lot, however, one of the reasons the Atari ST got a (much simpler) blitter as well in later releases.

3D Games are CPU-heavy, or rather performance is driven how fast you can do vector arithmetics and trigonometric functions (which would mainly be done by table lookups in older games) - Agnus doesn't help here, even a 68881 wouldn't help much, as fixed-point integer maths done by a 68k are still faster. We're talking mainly integer operations here, and that is driven by raw CPU speed and bus contention.

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.