I've only got superficial knowledge in this regard, so please take it with a grain of salt, but: the way I understand it is that PCIE has full direct memory access, so devices connected through it can use zero copy and similar techniques to access and process data much faster, especially with lower latencies than over regular USB. Using USB might/will require copying the data to transfer/read from and to different buffers, between user/kernel space, etc.

USB doesn’t provide any DMA (until USB 4) and requires more host cpu resources to meet the same bandwidth. It also has less consistent performance by virtue of the USB protocol itself.