I think the best bet is for the FPGA on the standalone board to expose some I2C or SPI buses (or SDIO), and then to use standard chips that connect to these buses for Ethernet (with TCP offload!), WiFi, BT, etc.
SATA really would require choosing an FPGA with a SATA hardware block already incorporated, or PCIe incorporated to connect an external controller. Could be a lot of work and increase the cost a lot. Personally I'd stick with the SD card readers, maybe have an internal slot and an external slot.