S-ATA is the way to go these days. Because the ATA interface has evolved to have some technical decency and it's the option with reasonable prices. SAS (serial SCSI) cost a fortune in comparison.
SATA would be nice but the high speed transceiver lines require a more expensive fpga and are limited. PCIe also need the same lines. A standalone fpga board may get these later but an SD card is adequate for most retro storage space requirements, it's tiny, it's common and it's low power (Hopefully no need to upgrade the power supply of a 500).
Regarding the 68060. To compete with the real thing any CPU would have to be as fast as 68060 @ 75 MHz. And then one has to make the decision if one should skip those instructions that Motorola did. Not doing it may cause incompatibilities but it may actually be a better processor. So perhaps an configuration option would be suitable.
Competing with the 68060 in speed shouldn't be a problem. Apollo will have several advantages:
much larger instruction fetch
stronger integer pipes
more instructions that can execute in both pipes (pOEP|sOEP)
code fusion/folding
some OoO instruction execution (MUL and DIV)
link stack (faster rts)
upgraded ISA and 64 bit MUL/DIV integer instructions return
much faster bit field instructions
much bigger caches (helps a lot with big programs)
faster memory
Phoenix will probably be available first without some of these advantages but most of these are in or provided for in the current Apollo design. The 68060 was a great processor for back in the day. It solved most of the 68k limitations with limited resources. It should have been the foundation for a series of new 68k processor designs but it was not fully optimized internally yet and was not given the resources to become more powerful. There is significant room for improvements.
