Question: I want to connect a PCIe 16x 3.0 GPU card to a Raspberry pi. I don't mind lo loose bandwidth, i just want to use the core GPU capabilities. So, the only idea that came out to my mind is to use the 26 GPIO RPi pins. I am concern about the GPIO/PCIe programing, do not have any idea neither an approach. Is this a crazy a idea ? can somebody help me to get a big picture of what i must to do ?

Answer: 
A few sites have tested the Pi's gpio speed and a quick search shows speeds on the order of hundreds of KHz. Not sure of the PCI 3 frequency off the top of my head but I believe each data line runs in the MHz range. 

The low frequency of the GPIO coupled with the coding overhead for each pin it would be impossible to bit bang the Pi fast enough.
If the Raspberry Pi has PCIe, then it is not exposed in a slot and it would require board modification which would be almost impossible for all but a very select few individuals without destroying it. Try the "lspci -vnnt" command and see if any devices are present. If PCIe is present, it is likely only there for the onboard Wi-Fi (much like things like the Galaxy S8).

The new RockPi 4 has the same mounting holes and form factor as the Raspberry Pi. It has the same compatible GPIO 40-pin header. It has a PCIe 2.0 x2 M.2 slot. You can adapt that to a full-sized PCIe slot. It will be bandwidth limited, but it should work. If you are gaming, then results might be poor. But for compute tasks that do not need much CPU-GPU communication, it should work great.

<https://shop.allnetchina.cn/collections/frontpage/products/rock-pi-4-model-b-board-only-with-dualband-2-4-5ghz-wlan-bluetooth-5-0>

You need to make sure that the slot has a PSU connector to supply 75W to the slot, and you might need extra PSU connectors straight to the graphics card if it is power hungry. You have to be careful because some slots create 3.3V from other voltages instead of from a SATA power connector, and if it is not designed for a GPU, it might overload and break. You either need one that is designed for a GPU, or one that takes the power directly from SATA power (not Molex, and SATA power that connects to the SFF-8643 connector does not guarantee anything, as some cables have Molex instead).

The Hikey 960 is the same deal but has incompatible mounting with the Raspberry Pi.

Something here might help: <https://click.intel.com/desktop-system-parts.html>

Those can go from M.2 to SFF-8639 and from there you might be able to get a SFF-8639 to PCIe slot adapter from Amazon or similar. I have seen whole kits from M.2 to PCIe but cannot vouch for their performance or reliability. Plus, some of them only wire one lane of PCIe from the M.2 slot. Make sure you get the 4-lane ones.