SATA is more for storage applications, PCIe high bandwith peripherals. I am a bit biased maybe because I have been in USB for more than 17 years but USB is high throughput too. But it has the extra perk that many classes of devices exist, storage, audio, video, … . And more and more USB is used for debug on silicon (more data than the slow JTAG protocol) which is relevant for SoC verification in simulation and later on the real silicon. My bet would be USB due to the wide range of uses.
Hardware and software advisor for tech startups. ASIC, FPGA, RPi, Arduino, AI, robots, drones, blockchain, Machine learning, vision processing, IoT and 3D printers are my fields of expertise.