I wish something like Pi Pico existed but with 1GHz clock, DDR3 memory interface and PCIe and few dozens of GPIO.

A RPi 4/5 has that? The OMAP 3/4 chips in Beaglebone is another alternative. Or Rockchip/Allwinner SoCs. Those are all Cortex A series though, but that can still be programmed bare metal if one wants. There are also Cortex M microcontrollers with support for SDRAM, like STM32H7. Or one can get an FPGA with DDR support like ECP5.

Xilinx Zync have PL for FPGA programmable logic, and PS with a few different ARM cores. They aren't as cheap as a Pi Pico though.