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Noise is a big one. The more levels you have, the more likely it is noise is going to turn a 0 to a 1 or a 1 to a 2, for example. It also requires more complicated switching transistors, because you can't rely on things being simply on or off, but rather have to generate a number of intermediary voltages.

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Differential signaling is one way to combat a lot of noise, which I do believe is used in the PCI spec already.

PCI[1] didn't use differential signalling, however it did use reflected-wave switching[2]. PCI express[3] does use differential signalling, as does a lot of other higher-speed busses like USB, SATA, or MIPI CSI-2/3[4].

[1]: https://en.wikipedia.org/wiki/Peripheral_Component_Interconn...

[2]: https://en.wikipedia.org/wiki/Reflected-wave_switching

[3]: https://en.wikipedia.org/wiki/PCI_Express#Lane

[4]: https://en.wikipedia.org/wiki/Camera_Serial_Interface

It doesn't eliminate all noise. You can play these games, but can never violate Shannon's. We hit Baud rates where channel loss was high enough that the SNR needed to be cut into to get more throughput. This cut the SNR so much that FEC was needed to maintain an acceptable error rate. PCIe lags IEEE 802.3 with these kinds of things. I'd call it bog standard but it's still bleeding edge.

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