Ive written bare-metal USB code on an MCU before, and I found it to be quite a shock compared to simple digital protocols like SPI or I2C. The physical and data link layers aren't much more complicated than, say, CAN, but beyond that you immediately run into a brick wall of descriptors, endpoints, and driver configuration. USB was designed from the ground up to be a plug-and-play ecosystem for PCs, and it really shows. Using the vendor-provided software as much as possible is definitely the way to go if you can.
Some half-remembered hints: You want bulk transfers for high throughput (don't even look at isochronous). USB is a master/slave protocol so if you're not getting peak throughput it's usually due to something on the host (PC) side. If the license (LGPL) is compatible with your needs, libusb is pretty easy to use. If you're not using the vendor driver, a hardware USB protocol analyzer is really helpful. USB in a NutShell[1] is a decent web reference for understanding the protocol.
Some half-remembered hints: You want bulk transfers for high throughput (don't even look at isochronous). USB is a master/slave protocol so if you're not getting peak throughput it's usually due to something on the host (PC) side. If the license (LGPL) is compatible with your needs, libusb is pretty easy to use. If you're not using the vendor driver, a hardware USB protocol analyzer is really helpful. USB in a NutShell[1] is a decent web reference for understanding the protocol.
[1] https://www.beyondlogic.org/usbnutshell/usb1.shtml