Can you share more details on your requirements for the GPIO interface? Would like to at least offer component details where we can.
The Diodes PI7C9X113SL is a transparent PCIe to PCI bus bridge for Gen1 speed. It will be backwards compatible with all PCIe slots (x1 -> x16). We use them in many of our designs. The current market price is insane. The drop in replacement is the PI7C9X118SL. Same device, different p/n. Don't ask...
There is some stock of this device available from Mouser. We can help to review your schematic if needed but is very simple to deploy. The bridge features an EEPROM to correct / program any of the default registers but to date, have shipped product with the eeprom blank. No compatibility issues to date using a 4L PCB with impedance controlled traces for the PCIe bus layout (Gen1 speed).
Fairly sure the PCIe to PCI bridge offers GPIO pins onboard. However, can certainly see the value to use a FPGA to bit bang out some state machine, etc. so the idea of a native PCIe or PCI device inside a FPGA is desirable.
Efinix is a good company to watch but had to side track for the past few months to Gowin as Efinix does not offer MPI DSI support where as Gowin does. Gowin is very cost effective for their devices (work with Edge Electronics in the USA for the best pricing if you can). We are sourcing through them but having the parts drop shipped to us from HK to save on the USA applied tariffs as we are in Canada.
The support from Gowin is top notch - the best we have seen from the assorted FPGA firms we have dealt with to date. Most of the FPGA vendors / factories do not reply back to us and others report - 'just read the docs and work it out' comments. After weeks and weeks of troubleshooting, we convinced the factory, every time, that they made mistakes.
What is our time worth ? To where do we send my invoice ? Tired of correcting other's mistakes in the semiconductor business and all this so we can buy their silicon?? We are far from being verilog and FPGA pros but getting very comfortable with Gowin tools. Just need to study their GAO. Have an excellent support contact in the USA if you need help.
Consider a Gowin FPGA with a hard CM3 CPU with enough LUTS to allow you to embed the PCI bus interface. Then the FPGA fabric and handle the GPIO or you can use the CM3 (will be slower).
One key concern is that what about the device driver to support this widget. You are ok to write code for Windows / Linux drivers ?
Also, a good website in case you have not seen it...
https://www.fpga4fun.com/PCI-Express.htmlJean has excellent articles on this website. We have learned a great deal about FPGA from here.