All you need is an expensive FPGA or some other IC that can convert to PCIe :)
Discussion
I knowwwwwww. I did some reasearch on a card I wanted to build a few years ago and PCIe is a total nightmare. It's similar to the automotive industry. Wait PCIe is a captured standard that's paid to access information... Sucks. Can't even get official dimensions, or parts, or even card widths from an official source. Have to literally use my calipers to measure the thickness of a PCB. Yeah it was probably available on some forum somewhere but that's no way to design a device.
There is an M.2 E-key that supports USB
usb is kind of buttcheecks too though. Everything is much cheaper and off the shelf I guess.
There is no perfect communication interface yet
usart, i2c, and spi are pretty decent, with the latter being quite fast for it's purpose.
Talking about that, smart cards use a half-duplex synchronous UART, except the fact that the frequency is ran through a fractional divider
Sometimes there’s parity. Sometimes not. Some versions of the protocol require you to pull the line low for a retransmit. Stopping the UART clock puts the card into sleep mode (usually.)
Another fun fact, contactless interface fully shuts down all systems including the NVM and CPU during transmit, with the only things being awake being the CL communications unit and RAM
I had looked into micros for doing the transfer but it's basically always done with an FPGA because of the fast multiplexed nature of the coms. No micro can keep up, even with DMA and some multiplexors/decoders.