Your question was why to use this over PCIe. Maybe I'm misunderstanding your question but as Syzygy is a connector standard, your question must have been about the connector. I think colloquially the "PCIe connector" refers to the finger and slot standard.
As for why to use single end low speed I/O, I guess it's about perspective. For some, an FPGA is something that sits on a PCIe bus or network. For a lot of people, it's a lot more than that. Something that talks to countless chips that maybe need spi, i2c, uart, or something custom.
For example, think about all those 1 wire LED strips and how it easy it would be to do that in HDL compared to the other approaches. Being and to work easily with bits vs bytes has huge advantages for custom interfaces. Another example: one time a group I was working with wanted to talk to battery management modules. Each one had a uart and they had to get daisy chained together, complicating things a lot. An FPGA with more than a few uarts is trivial and could've talked to each one independently. Even the highest end micros have maybe at most 20. You could fit 16 on 1 of these connectors. The UART block from Xilinx is on the order of 100 flops. You could have literally hundreds of uarts. Not that I have seen a need for that, but who knows, maybe someone does.
Getting rambley but another option is for test devices. Let's say you have a device that has a low speed interface and you want to test a lot of them at a time. You could use a bunch of multiplexors and time division control logic, or slap down an FPGA and do them all at once.
As for why to use single end low speed I/O, I guess it's about perspective. For some, an FPGA is something that sits on a PCIe bus or network. For a lot of people, it's a lot more than that. Something that talks to countless chips that maybe need spi, i2c, uart, or something custom.
For example, think about all those 1 wire LED strips and how it easy it would be to do that in HDL compared to the other approaches. Being and to work easily with bits vs bytes has huge advantages for custom interfaces. Another example: one time a group I was working with wanted to talk to battery management modules. Each one had a uart and they had to get daisy chained together, complicating things a lot. An FPGA with more than a few uarts is trivial and could've talked to each one independently. Even the highest end micros have maybe at most 20. You could fit 16 on 1 of these connectors. The UART block from Xilinx is on the order of 100 flops. You could have literally hundreds of uarts. Not that I have seen a need for that, but who knows, maybe someone does.
Getting rambley but another option is for test devices. Let's say you have a device that has a low speed interface and you want to test a lot of them at a time. You could use a bunch of multiplexors and time division control logic, or slap down an FPGA and do them all at once.